Seroconversion

Blue = seroconversion+, Orange = seroconversion-.

   
    IND IND (neo+) IND (neo-) MLW
  0 204        104         99  46
  1  78         45         33  10

  seroconv Observed.mean Observed.sd Observed.country
1        0         47.09       14.38              IND
2        1         41.85       12.55              IND
3        0         45.78       13.77       IND (neo+)
4        1         43.16       11.49       IND (neo+)
5        0         48.53       14.99       IND (neo-)
6        1         40.06       13.84       IND (neo-)
7        0         57.02       11.16              MLW
8        1          48.5       13.39              MLW

                   [,1]
IND            0.006537
MLW            0.056632
IND_exposed    0.134577
IND_nonexposed 0.000144

RV-IgA

               rho        p   n
IND        -0.1079 0.070401 282
IND (neo+) -0.0140 0.865418 149
IND (neo-) -0.1587 0.069136 132
MLW        -0.0597 0.662209  56

Dose 1 shedding

Blue = shed+, Orange = shed-.

   
    IND IND (neo+) IND (neo-) MLW
  0 207        122         83  26
  1  74         25         49  21

  dose1_shedding Observed.mean Observed.sd Observed.country
1              0         46.38        13.4              IND
2              1         43.82       15.72              IND
3              0         45.54       13.17       IND (neo+)
4              1         43.08       13.29       IND (neo+)
5              0         47.71       13.87       IND (neo-)
6              1          44.2       16.95       IND (neo-)
7              0         57.65       11.82              MLW
8              1         53.62       14.12              MLW

                   [,1]
IND            0.112668
MLW            0.265382
IND_exposed    0.126043
IND_nonexposed 0.048244

Seroconversion

                    R2     p   n    country full        outcome
IND_BS3      0.7608001 0.027 282        IND    1 seroconversion
INDexp_BS3   0.6161644 0.530 149 IND (neo+)    0 seroconversion
INDunexp_BS3 2.0767500 0.013 132 IND (neo-)    0 seroconversion
MLW_BS3      3.0203755 0.091  56        MLW    1 seroconversion

RV-IgA

                    R2     p   n    country full           outcome
IND_BS3      0.5240005 0.145 282        IND    1 RV-IgA (post-ORV)
INDexp_BS3   0.4468910 0.755 149 IND (neo+)    0 RV-IgA (post-ORV)
INDunexp_BS3 1.4834609 0.041 132 IND (neo-)    0 RV-IgA (post-ORV)
MLW_BS3      2.2557640 0.278  56        MLW    1 RV-IgA (post-ORV)

Dose 1 shedding

                    R2     p   n    country full         outcome
IND_BS3      0.4270526 0.262 281        IND    1 dose 1 shedding
INDexp_BS3   0.7857308 0.303 147 IND (neo+)    0 dose 1 shedding
INDunexp_BS3 1.0419810 0.188 132 IND (neo-)    0 dose 1 shedding
MLW_BS3      0.7838829 0.920  47        MLW    1 dose 1 shedding

Seroconversion

[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:30:37 INFO::Writing function arguments to log file
2023-03-15 14:30:38 INFO::Verifying options selected are valid
2023-03-15 14:30:38 INFO::Determining format of input files
2023-03-15 14:30:38 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:30:38 INFO::Formula for fixed effects: expr ~  seroconv
2023-03-15 14:30:38 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:30:38 INFO::Total samples in data: 282
2023-03-15 14:30:38 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:30:38 INFO::Total filtered features: 0
2023-03-15 14:30:38 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:30:38 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:30:38 INFO::Filtered feature names from variance filtering:
2023-03-15 14:30:38 INFO::Running selected normalization method: NONE
2023-03-15 14:30:38 INFO::Bypass z-score application to metadata
2023-03-15 14:30:38 INFO::Running selected transform method: AST
2023-03-15 14:30:38 INFO::Running selected analysis method: LM
2023-03-15 14:30:38 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:30:38 INFO::Fitting model to feature number 2, t562
2023-03-15 14:30:38 INFO::Fitting model to feature number 3, t573
2023-03-15 14:30:38 INFO::Fitting model to feature number 4, t817
2023-03-15 14:30:38 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:30:38 INFO::Fitting model to feature number 6, t823
2023-03-15 14:30:38 INFO::Fitting model to feature number 7, t821
2023-03-15 14:30:38 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:30:38 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:30:38 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:30:38 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:30:38 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:30:38 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:30:38 INFO::Fitting model to feature number 14, t550
2023-03-15 14:30:38 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:30:38 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:30:38 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:30:38 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:30:38 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:30:38 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:30:38 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:30:38 INFO::Fitting model to feature number 22, t729
2023-03-15 14:30:38 INFO::Fitting model to feature number 23, t907
2023-03-15 14:30:38 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:30:38 INFO::Fitting model to feature number 25, t853
2023-03-15 14:30:38 INFO::Fitting model to feature number 26, t197
2023-03-15 14:30:38 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:30:38 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:30:38 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:30:38 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:30:38 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:30:38 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:30:38 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:30:38 INFO::Fitting model to feature number 34, t584
2023-03-15 14:30:38 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:30:38 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:30:38 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:30:38 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:30:38 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:30:38 INFO::Fitting model to feature number 40, t624
2023-03-15 14:30:38 INFO::Fitting model to feature number 41, t545
2023-03-15 14:30:38 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:30:38 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:30:38 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:30:38 INFO::Fitting model to feature number 45, t582
2023-03-15 14:30:38 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:30:38 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:30:38 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:30:38 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:30:38 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:30:38 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:30:38 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:30:38 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:30:38 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:30:38 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:30:38 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:30:38 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:30:38 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:30:38 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:30:38 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:30:38 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:30:38 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:30:38 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:30:38 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:30:38 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:30:38 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:30:38 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:30:38 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:30:38 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:30:38 INFO::Fitting model to feature number 70, t287
2023-03-15 14:30:38 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:30:38 INFO::Fitting model to feature number 72, t604330
2023-03-15 14:30:38 INFO::Fitting model to feature number 73, t143361
2023-03-15 14:30:38 INFO::Fitting model to feature number 74, t2823316
2023-03-15 14:30:38 INFO::Fitting model to feature number 75, t2093857
2023-03-15 14:30:38 INFO::Fitting model to feature number 76, t84030
2023-03-15 14:30:38 INFO::Fitting model to feature number 77, t1464
2023-03-15 14:30:38 INFO::Fitting model to feature number 78, t1297617
2023-03-15 14:30:38 INFO::Fitting model to feature number 79, t2714355
2023-03-15 14:30:38 INFO::Fitting model to feature number 80, t83655
2023-03-15 14:30:38 INFO::Fitting model to feature number 81, t2774055
2023-03-15 14:30:38 INFO::Fitting model to feature number 82, t1270
2023-03-15 14:30:38 INFO::Fitting model to feature number 83, t39485
2023-03-15 14:30:38 INFO::Fitting model to feature number 84, t1583
2023-03-15 14:30:38 INFO::Fitting model to feature number 85, t71999
2023-03-15 14:30:38 INFO::Counting total values for each feature
2023-03-15 14:30:38 INFO::Writing residuals to file maaslin_outputs/seroconv_India_unadjusted/residuals.rds
2023-03-15 14:30:38 INFO::Writing fitted values to file maaslin_outputs/seroconv_India_unadjusted/fitted.rds
2023-03-15 14:30:38 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/seroconv_India_unadjusted/all_results.tsv
2023-03-15 14:30:38 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/seroconv_India_unadjusted/significant_results.tsv
2023-03-15 14:30:38 INFO::Writing heatmap of significant results to file: maaslin_outputs/seroconv_India_unadjusted/heatmap.pdf
[1] "There are no associations to plot!"
[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:30:38 INFO::Writing function arguments to log file
2023-03-15 14:30:38 INFO::Verifying options selected are valid
2023-03-15 14:30:38 INFO::Determining format of input files
2023-03-15 14:30:38 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:30:38 INFO::Formula for fixed effects: expr ~  seroconv + age_at_first_dose + antibiotic_exposure + birth_weight + breastfed_child + mode_delivery
2023-03-15 14:30:38 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:30:38 INFO::Total samples in data: 282
2023-03-15 14:30:38 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:30:38 INFO::Total filtered features: 0
2023-03-15 14:30:38 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:30:38 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:30:38 INFO::Filtered feature names from variance filtering:
2023-03-15 14:30:38 INFO::Running selected normalization method: NONE
2023-03-15 14:30:38 INFO::Bypass z-score application to metadata
2023-03-15 14:30:38 INFO::Running selected transform method: AST
2023-03-15 14:30:38 INFO::Running selected analysis method: LM
2023-03-15 14:30:38 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:30:38 INFO::Fitting model to feature number 2, t562
2023-03-15 14:30:38 INFO::Fitting model to feature number 3, t573
2023-03-15 14:30:38 INFO::Fitting model to feature number 4, t817
2023-03-15 14:30:38 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:30:38 INFO::Fitting model to feature number 6, t823
2023-03-15 14:30:38 INFO::Fitting model to feature number 7, t821
2023-03-15 14:30:38 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:30:38 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:30:38 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:30:38 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:30:38 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:30:38 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:30:38 INFO::Fitting model to feature number 14, t550
2023-03-15 14:30:38 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:30:38 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:30:38 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:30:38 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:30:38 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:30:38 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:30:38 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:30:38 INFO::Fitting model to feature number 22, t729
2023-03-15 14:30:38 INFO::Fitting model to feature number 23, t907
2023-03-15 14:30:38 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:30:38 INFO::Fitting model to feature number 25, t853
2023-03-15 14:30:39 INFO::Fitting model to feature number 26, t197
2023-03-15 14:30:39 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:30:39 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:30:39 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:30:39 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:30:39 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:30:39 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:30:39 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:30:39 INFO::Fitting model to feature number 34, t584
2023-03-15 14:30:39 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:30:39 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:30:39 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:30:39 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:30:39 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:30:39 INFO::Fitting model to feature number 40, t624
2023-03-15 14:30:39 INFO::Fitting model to feature number 41, t545
2023-03-15 14:30:39 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:30:39 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:30:39 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:30:39 INFO::Fitting model to feature number 45, t582
2023-03-15 14:30:39 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:30:39 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:30:39 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:30:39 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:30:39 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:30:39 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:30:39 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:30:39 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:30:39 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:30:39 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:30:39 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:30:39 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:30:39 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:30:39 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:30:39 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:30:39 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:30:39 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:30:39 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:30:39 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:30:39 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:30:39 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:30:39 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:30:39 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:30:39 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:30:39 INFO::Fitting model to feature number 70, t287
2023-03-15 14:30:39 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:30:39 INFO::Fitting model to feature number 72, t604330
2023-03-15 14:30:39 INFO::Fitting model to feature number 73, t143361
2023-03-15 14:30:39 INFO::Fitting model to feature number 74, t2823316
2023-03-15 14:30:39 INFO::Fitting model to feature number 75, t2093857
2023-03-15 14:30:39 INFO::Fitting model to feature number 76, t84030
2023-03-15 14:30:39 INFO::Fitting model to feature number 77, t1464
2023-03-15 14:30:39 INFO::Fitting model to feature number 78, t1297617
2023-03-15 14:30:39 INFO::Fitting model to feature number 79, t2714355
2023-03-15 14:30:39 INFO::Fitting model to feature number 80, t83655
2023-03-15 14:30:39 INFO::Fitting model to feature number 81, t2774055
2023-03-15 14:30:39 INFO::Fitting model to feature number 82, t1270
2023-03-15 14:30:39 INFO::Fitting model to feature number 83, t39485
2023-03-15 14:30:39 INFO::Fitting model to feature number 84, t1583
2023-03-15 14:30:39 INFO::Fitting model to feature number 85, t71999
2023-03-15 14:30:39 INFO::Counting total values for each feature
2023-03-15 14:30:39 INFO::Writing residuals to file maaslin_outputs/seroconv_India_adjusted/residuals.rds
2023-03-15 14:30:39 INFO::Writing fitted values to file maaslin_outputs/seroconv_India_adjusted/fitted.rds
2023-03-15 14:30:39 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/seroconv_India_adjusted/all_results.tsv
2023-03-15 14:30:39 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/seroconv_India_adjusted/significant_results.tsv
2023-03-15 14:30:39 INFO::Writing heatmap of significant results to file: maaslin_outputs/seroconv_India_adjusted/heatmap.pdf

[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:30:55 INFO::Writing function arguments to log file
2023-03-15 14:30:55 INFO::Verifying options selected are valid
2023-03-15 14:30:55 INFO::Determining format of input files
2023-03-15 14:30:55 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:30:55 INFO::Formula for fixed effects: expr ~  seroconv
2023-03-15 14:30:55 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:30:55 INFO::Total samples in data: 149
2023-03-15 14:30:55 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:30:55 INFO::Total filtered features: 0
2023-03-15 14:30:55 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:30:55 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:30:55 INFO::Filtered feature names from variance filtering:
2023-03-15 14:30:55 INFO::Running selected normalization method: NONE
2023-03-15 14:30:55 INFO::Bypass z-score application to metadata
2023-03-15 14:30:55 INFO::Running selected transform method: AST
2023-03-15 14:30:55 INFO::Running selected analysis method: LM
2023-03-15 14:30:55 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:30:55 INFO::Fitting model to feature number 2, t562
2023-03-15 14:30:55 INFO::Fitting model to feature number 3, t573
2023-03-15 14:30:55 INFO::Fitting model to feature number 4, t817
2023-03-15 14:30:56 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:30:56 INFO::Fitting model to feature number 6, t823
2023-03-15 14:30:56 INFO::Fitting model to feature number 7, t821
2023-03-15 14:30:56 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:30:56 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:30:56 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:30:56 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:30:56 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:30:56 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:30:56 INFO::Fitting model to feature number 14, t550
2023-03-15 14:30:56 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:30:56 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:30:56 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:30:56 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:30:56 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:30:56 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:30:56 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:30:56 INFO::Fitting model to feature number 22, t729
2023-03-15 14:30:56 INFO::Fitting model to feature number 23, t907
2023-03-15 14:30:56 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:30:56 INFO::Fitting model to feature number 25, t853
2023-03-15 14:30:56 INFO::Fitting model to feature number 26, t197
2023-03-15 14:30:56 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:30:56 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:30:56 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:30:56 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:30:56 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:30:56 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:30:56 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:30:56 INFO::Fitting model to feature number 34, t584
2023-03-15 14:30:56 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:30:56 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:30:56 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:30:56 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:30:56 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:30:56 INFO::Fitting model to feature number 40, t624
2023-03-15 14:30:56 INFO::Fitting model to feature number 41, t545
2023-03-15 14:30:56 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:30:56 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:30:56 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:30:56 INFO::Fitting model to feature number 45, t582
2023-03-15 14:30:56 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:30:56 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:30:56 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:30:56 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:30:56 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:30:56 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:30:56 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:30:56 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:30:56 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:30:56 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:30:56 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:30:56 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:30:56 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:30:56 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:30:56 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:30:56 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:30:56 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:30:56 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:30:56 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:30:56 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:30:56 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:30:56 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:30:56 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:30:56 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:30:56 INFO::Fitting model to feature number 70, t287
2023-03-15 14:30:56 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:30:56 INFO::Fitting model to feature number 72, t604330
2023-03-15 14:30:56 INFO::Fitting model to feature number 73, t143361
2023-03-15 14:30:56 INFO::Fitting model to feature number 74, t2823316
2023-03-15 14:30:56 INFO::Fitting model to feature number 75, t2093857
2023-03-15 14:30:56 INFO::Fitting model to feature number 76, t84030
2023-03-15 14:30:56 INFO::Fitting model to feature number 77, t1464
2023-03-15 14:30:56 INFO::Fitting model to feature number 78, t1297617
2023-03-15 14:30:56 INFO::Fitting model to feature number 79, t2714355
2023-03-15 14:30:56 INFO::Fitting model to feature number 80, t83655
2023-03-15 14:30:56 INFO::Fitting model to feature number 81, t2774055
2023-03-15 14:30:56 INFO::Fitting model to feature number 82, t1270
2023-03-15 14:30:56 INFO::Fitting model to feature number 83, t39485
2023-03-15 14:30:56 INFO::Fitting model to feature number 84, t1583
2023-03-15 14:30:56 INFO::Fitting model to feature number 85, t71999
2023-03-15 14:30:56 INFO::Counting total values for each feature
2023-03-15 14:30:56 INFO::Writing residuals to file maaslin_outputs/seroconv_India (exposed)_unadjusted/residuals.rds
2023-03-15 14:30:56 INFO::Writing fitted values to file maaslin_outputs/seroconv_India (exposed)_unadjusted/fitted.rds
2023-03-15 14:30:56 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/seroconv_India (exposed)_unadjusted/all_results.tsv
2023-03-15 14:30:56 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/seroconv_India (exposed)_unadjusted/significant_results.tsv
2023-03-15 14:30:56 INFO::Writing heatmap of significant results to file: maaslin_outputs/seroconv_India (exposed)_unadjusted/heatmap.pdf
[1] "There are no associations to plot!"
[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:30:56 INFO::Writing function arguments to log file
2023-03-15 14:30:56 INFO::Verifying options selected are valid
2023-03-15 14:30:56 INFO::Determining format of input files
2023-03-15 14:30:56 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:30:56 INFO::Formula for fixed effects: expr ~  seroconv + age_at_first_dose + antibiotic_exposure + birth_weight + breastfed_child + mode_delivery
2023-03-15 14:30:56 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:30:56 INFO::Total samples in data: 149
2023-03-15 14:30:56 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:30:56 INFO::Total filtered features: 0
2023-03-15 14:30:56 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:30:56 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:30:56 INFO::Filtered feature names from variance filtering:
2023-03-15 14:30:56 INFO::Running selected normalization method: NONE
2023-03-15 14:30:56 INFO::Bypass z-score application to metadata
2023-03-15 14:30:56 INFO::Running selected transform method: AST
2023-03-15 14:30:56 INFO::Running selected analysis method: LM
2023-03-15 14:30:56 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:30:56 INFO::Fitting model to feature number 2, t562
2023-03-15 14:30:56 INFO::Fitting model to feature number 3, t573
2023-03-15 14:30:56 INFO::Fitting model to feature number 4, t817
2023-03-15 14:30:56 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:30:56 INFO::Fitting model to feature number 6, t823
2023-03-15 14:30:56 INFO::Fitting model to feature number 7, t821
2023-03-15 14:30:56 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:30:56 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:30:56 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:30:56 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:30:56 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:30:56 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:30:56 INFO::Fitting model to feature number 14, t550
2023-03-15 14:30:56 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:30:56 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:30:56 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:30:56 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:30:56 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:30:56 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:30:56 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:30:56 INFO::Fitting model to feature number 22, t729
2023-03-15 14:30:56 INFO::Fitting model to feature number 23, t907
2023-03-15 14:30:56 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:30:56 INFO::Fitting model to feature number 25, t853
2023-03-15 14:30:56 INFO::Fitting model to feature number 26, t197
2023-03-15 14:30:56 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:30:56 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:30:56 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:30:56 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:30:56 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:30:56 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:30:56 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:30:56 INFO::Fitting model to feature number 34, t584
2023-03-15 14:30:56 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:30:56 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:30:56 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:30:56 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:30:56 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:30:56 INFO::Fitting model to feature number 40, t624
2023-03-15 14:30:56 INFO::Fitting model to feature number 41, t545
2023-03-15 14:30:56 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:30:56 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:30:56 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:30:56 INFO::Fitting model to feature number 45, t582
2023-03-15 14:30:56 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:30:56 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:30:56 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:30:56 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:30:57 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:30:57 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:30:57 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:30:57 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:30:57 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:30:57 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:30:57 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:30:57 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:30:57 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:30:57 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:30:57 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:30:57 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:30:57 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:30:57 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:30:57 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:30:57 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:30:57 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:30:57 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:30:57 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:30:57 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:30:57 INFO::Fitting model to feature number 70, t287
2023-03-15 14:30:57 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:30:57 INFO::Fitting model to feature number 72, t604330
2023-03-15 14:30:57 INFO::Fitting model to feature number 73, t143361
2023-03-15 14:30:57 INFO::Fitting model to feature number 74, t2823316
2023-03-15 14:30:57 INFO::Fitting model to feature number 75, t2093857
2023-03-15 14:30:57 INFO::Fitting model to feature number 76, t84030
2023-03-15 14:30:57 INFO::Fitting model to feature number 77, t1464
2023-03-15 14:30:57 INFO::Fitting model to feature number 78, t1297617
2023-03-15 14:30:57 INFO::Fitting model to feature number 79, t2714355
2023-03-15 14:30:57 INFO::Fitting model to feature number 80, t83655
2023-03-15 14:30:57 INFO::Fitting model to feature number 81, t2774055
2023-03-15 14:30:57 INFO::Fitting model to feature number 82, t1270
2023-03-15 14:30:57 INFO::Fitting model to feature number 83, t39485
2023-03-15 14:30:57 INFO::Fitting model to feature number 84, t1583
2023-03-15 14:30:57 INFO::Fitting model to feature number 85, t71999
2023-03-15 14:30:57 INFO::Counting total values for each feature
2023-03-15 14:30:57 INFO::Writing residuals to file maaslin_outputs/seroconv_India (exposed)_adjusted/residuals.rds
2023-03-15 14:30:57 INFO::Writing fitted values to file maaslin_outputs/seroconv_India (exposed)_adjusted/fitted.rds
2023-03-15 14:30:57 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/seroconv_India (exposed)_adjusted/all_results.tsv
2023-03-15 14:30:57 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/seroconv_India (exposed)_adjusted/significant_results.tsv
2023-03-15 14:30:57 INFO::Writing heatmap of significant results to file: maaslin_outputs/seroconv_India (exposed)_adjusted/heatmap.pdf

[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:31:05 INFO::Writing function arguments to log file
2023-03-15 14:31:05 INFO::Verifying options selected are valid
2023-03-15 14:31:05 INFO::Determining format of input files
2023-03-15 14:31:05 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:31:05 INFO::Formula for fixed effects: expr ~  seroconv
2023-03-15 14:31:05 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:31:05 INFO::Total samples in data: 132
2023-03-15 14:31:05 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:31:05 INFO::Total filtered features: 0
2023-03-15 14:31:05 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:31:05 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:31:05 INFO::Filtered feature names from variance filtering:
2023-03-15 14:31:05 INFO::Running selected normalization method: NONE
2023-03-15 14:31:05 INFO::Bypass z-score application to metadata
2023-03-15 14:31:05 INFO::Running selected transform method: AST
2023-03-15 14:31:05 INFO::Running selected analysis method: LM
2023-03-15 14:31:05 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:31:05 INFO::Fitting model to feature number 2, t562
2023-03-15 14:31:05 INFO::Fitting model to feature number 3, t573
2023-03-15 14:31:05 INFO::Fitting model to feature number 4, t817
2023-03-15 14:31:05 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:31:05 INFO::Fitting model to feature number 6, t823
2023-03-15 14:31:05 INFO::Fitting model to feature number 7, t821
2023-03-15 14:31:05 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:31:05 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:31:05 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:31:05 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:31:05 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:31:05 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:31:05 INFO::Fitting model to feature number 14, t550
2023-03-15 14:31:05 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:31:05 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:31:05 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:31:05 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:31:05 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:31:05 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:31:05 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:31:05 INFO::Fitting model to feature number 22, t729
2023-03-15 14:31:05 INFO::Fitting model to feature number 23, t907
2023-03-15 14:31:05 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:31:05 INFO::Fitting model to feature number 25, t853
2023-03-15 14:31:05 INFO::Fitting model to feature number 26, t197
2023-03-15 14:31:05 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:31:05 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:31:05 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:31:05 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:31:05 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:31:05 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:31:05 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:31:05 INFO::Fitting model to feature number 34, t584
2023-03-15 14:31:05 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:31:05 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:31:05 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:31:05 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:31:05 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:31:05 INFO::Fitting model to feature number 40, t624
2023-03-15 14:31:05 INFO::Fitting model to feature number 41, t545
2023-03-15 14:31:05 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:31:05 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:31:05 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:31:05 INFO::Fitting model to feature number 45, t582
2023-03-15 14:31:05 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:31:05 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:31:05 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:31:05 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:31:05 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:31:05 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:31:05 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:31:05 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:31:05 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:31:05 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:31:05 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:31:05 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:31:05 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:31:05 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:31:05 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:31:05 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:31:05 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:31:05 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:31:05 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:31:05 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:31:05 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:31:05 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:31:05 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:31:05 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:31:05 INFO::Fitting model to feature number 70, t287
2023-03-15 14:31:05 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:31:05 INFO::Fitting model to feature number 72, t901
2023-03-15 14:31:05 INFO::Fitting model to feature number 73, t604330
2023-03-15 14:31:05 INFO::Fitting model to feature number 74, t143361
2023-03-15 14:31:05 INFO::Fitting model to feature number 75, t2823316
2023-03-15 14:31:05 INFO::Fitting model to feature number 76, t2093857
2023-03-15 14:31:05 INFO::Fitting model to feature number 77, t84030
2023-03-15 14:31:05 INFO::Fitting model to feature number 78, t1464
2023-03-15 14:31:05 INFO::Fitting model to feature number 79, t1297617
2023-03-15 14:31:05 INFO::Fitting model to feature number 80, t2714355
2023-03-15 14:31:05 INFO::Fitting model to feature number 81, t83655
2023-03-15 14:31:05 INFO::Fitting model to feature number 82, t2774055
2023-03-15 14:31:05 INFO::Fitting model to feature number 83, t1270
2023-03-15 14:31:05 INFO::Fitting model to feature number 84, t39485
2023-03-15 14:31:05 INFO::Fitting model to feature number 85, t1583
2023-03-15 14:31:05 INFO::Fitting model to feature number 86, t71999
2023-03-15 14:31:05 INFO::Counting total values for each feature
2023-03-15 14:31:05 INFO::Writing residuals to file maaslin_outputs/seroconv_India (unexposed)_unadjusted/residuals.rds
2023-03-15 14:31:05 INFO::Writing fitted values to file maaslin_outputs/seroconv_India (unexposed)_unadjusted/fitted.rds
2023-03-15 14:31:05 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/seroconv_India (unexposed)_unadjusted/all_results.tsv
2023-03-15 14:31:05 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/seroconv_India (unexposed)_unadjusted/significant_results.tsv
2023-03-15 14:31:05 INFO::Writing heatmap of significant results to file: maaslin_outputs/seroconv_India (unexposed)_unadjusted/heatmap.pdf
[1] "There are no associations to plot!"
[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:31:05 INFO::Writing function arguments to log file
2023-03-15 14:31:05 INFO::Verifying options selected are valid
2023-03-15 14:31:05 INFO::Determining format of input files
2023-03-15 14:31:05 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:31:05 INFO::Formula for fixed effects: expr ~  seroconv + age_at_first_dose + antibiotic_exposure + birth_weight + breastfed_child + mode_delivery
2023-03-15 14:31:05 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:31:05 INFO::Total samples in data: 132
2023-03-15 14:31:05 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:31:05 INFO::Total filtered features: 0
2023-03-15 14:31:05 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:31:05 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:31:05 INFO::Filtered feature names from variance filtering:
2023-03-15 14:31:05 INFO::Running selected normalization method: NONE
2023-03-15 14:31:05 INFO::Bypass z-score application to metadata
2023-03-15 14:31:05 INFO::Running selected transform method: AST
2023-03-15 14:31:05 INFO::Running selected analysis method: LM
2023-03-15 14:31:05 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:31:05 INFO::Fitting model to feature number 2, t562
2023-03-15 14:31:05 INFO::Fitting model to feature number 3, t573
2023-03-15 14:31:05 INFO::Fitting model to feature number 4, t817
2023-03-15 14:31:05 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:31:05 INFO::Fitting model to feature number 6, t823
2023-03-15 14:31:05 INFO::Fitting model to feature number 7, t821
2023-03-15 14:31:05 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:31:06 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:31:06 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:31:06 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:31:06 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:31:06 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:31:06 INFO::Fitting model to feature number 14, t550
2023-03-15 14:31:06 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:31:06 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:31:06 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:31:06 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:31:06 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:31:06 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:31:06 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:31:06 INFO::Fitting model to feature number 22, t729
2023-03-15 14:31:06 INFO::Fitting model to feature number 23, t907
2023-03-15 14:31:06 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:31:06 INFO::Fitting model to feature number 25, t853
2023-03-15 14:31:06 INFO::Fitting model to feature number 26, t197
2023-03-15 14:31:06 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:31:06 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:31:06 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:31:06 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:31:06 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:31:06 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:31:06 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:31:06 INFO::Fitting model to feature number 34, t584
2023-03-15 14:31:06 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:31:06 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:31:06 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:31:06 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:31:06 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:31:06 INFO::Fitting model to feature number 40, t624
2023-03-15 14:31:06 INFO::Fitting model to feature number 41, t545
2023-03-15 14:31:06 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:31:06 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:31:06 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:31:06 INFO::Fitting model to feature number 45, t582
2023-03-15 14:31:06 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:31:06 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:31:06 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:31:06 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:31:06 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:31:06 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:31:06 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:31:06 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:31:06 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:31:06 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:31:06 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:31:06 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:31:06 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:31:06 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:31:06 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:31:06 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:31:06 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:31:06 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:31:06 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:31:06 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:31:06 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:31:06 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:31:06 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:31:06 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:31:06 INFO::Fitting model to feature number 70, t287
2023-03-15 14:31:06 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:31:06 INFO::Fitting model to feature number 72, t901
2023-03-15 14:31:06 INFO::Fitting model to feature number 73, t604330
2023-03-15 14:31:06 INFO::Fitting model to feature number 74, t143361
2023-03-15 14:31:06 INFO::Fitting model to feature number 75, t2823316
2023-03-15 14:31:06 INFO::Fitting model to feature number 76, t2093857
2023-03-15 14:31:06 INFO::Fitting model to feature number 77, t84030
2023-03-15 14:31:06 INFO::Fitting model to feature number 78, t1464
2023-03-15 14:31:06 INFO::Fitting model to feature number 79, t1297617
2023-03-15 14:31:06 INFO::Fitting model to feature number 80, t2714355
2023-03-15 14:31:06 INFO::Fitting model to feature number 81, t83655
2023-03-15 14:31:06 INFO::Fitting model to feature number 82, t2774055
2023-03-15 14:31:06 INFO::Fitting model to feature number 83, t1270
2023-03-15 14:31:06 INFO::Fitting model to feature number 84, t39485
2023-03-15 14:31:06 INFO::Fitting model to feature number 85, t1583
2023-03-15 14:31:06 INFO::Fitting model to feature number 86, t71999
2023-03-15 14:31:06 INFO::Counting total values for each feature
2023-03-15 14:31:06 INFO::Writing residuals to file maaslin_outputs/seroconv_India (unexposed)_adjusted/residuals.rds
2023-03-15 14:31:06 INFO::Writing fitted values to file maaslin_outputs/seroconv_India (unexposed)_adjusted/fitted.rds
2023-03-15 14:31:06 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/seroconv_India (unexposed)_adjusted/all_results.tsv
2023-03-15 14:31:06 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/seroconv_India (unexposed)_adjusted/significant_results.tsv
2023-03-15 14:31:06 INFO::Writing heatmap of significant results to file: maaslin_outputs/seroconv_India (unexposed)_adjusted/heatmap.pdf

[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:31:09 INFO::Writing function arguments to log file
2023-03-15 14:31:09 INFO::Verifying options selected are valid
2023-03-15 14:31:09 INFO::Determining format of input files
2023-03-15 14:31:09 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:31:09 INFO::Formula for fixed effects: expr ~  seroconv
2023-03-15 14:31:09 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:31:09 INFO::Total samples in data: 56
2023-03-15 14:31:09 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:31:09 INFO::Total filtered features: 0
2023-03-15 14:31:09 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:31:09 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:31:09 INFO::Filtered feature names from variance filtering:
2023-03-15 14:31:09 INFO::Running selected normalization method: NONE
2023-03-15 14:31:09 INFO::Bypass z-score application to metadata
2023-03-15 14:31:09 INFO::Running selected transform method: AST
2023-03-15 14:31:09 INFO::Running selected analysis method: LM
2023-03-15 14:31:09 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:31:09 INFO::Fitting model to feature number 2, t562
2023-03-15 14:31:09 INFO::Fitting model to feature number 3, t573
2023-03-15 14:31:09 INFO::Fitting model to feature number 4, t817
2023-03-15 14:31:09 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:31:09 INFO::Fitting model to feature number 6, t823
2023-03-15 14:31:09 INFO::Fitting model to feature number 7, t821
2023-03-15 14:31:09 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:31:09 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:31:09 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:31:09 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:31:09 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:31:09 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:31:09 INFO::Fitting model to feature number 14, t550
2023-03-15 14:31:09 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:31:09 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:31:09 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:31:09 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:31:09 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:31:09 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:31:09 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:31:09 INFO::Fitting model to feature number 22, t729
2023-03-15 14:31:09 INFO::Fitting model to feature number 23, t907
2023-03-15 14:31:09 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:31:09 INFO::Fitting model to feature number 25, t853
2023-03-15 14:31:09 INFO::Fitting model to feature number 26, t197
2023-03-15 14:31:09 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:31:09 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:31:09 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:31:09 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:31:09 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:31:09 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:31:09 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:31:09 INFO::Fitting model to feature number 34, t584
2023-03-15 14:31:09 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:31:09 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:31:09 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:31:09 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:31:09 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:31:09 INFO::Fitting model to feature number 40, t624
2023-03-15 14:31:09 INFO::Fitting model to feature number 41, t545
2023-03-15 14:31:09 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:31:09 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:31:09 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:31:09 INFO::Fitting model to feature number 45, t582
2023-03-15 14:31:09 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:31:09 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:31:09 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:31:09 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:31:09 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:31:09 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:31:09 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:31:09 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:31:09 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:31:09 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:31:09 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:31:09 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:31:09 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:31:09 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:31:09 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:31:09 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:31:09 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:31:09 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:31:09 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:31:09 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:31:09 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:31:09 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:31:09 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:31:09 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:31:09 INFO::Fitting model to feature number 70, t287
2023-03-15 14:31:09 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:31:09 INFO::Fitting model to feature number 72, t901
2023-03-15 14:31:09 INFO::Fitting model to feature number 73, t604330
2023-03-15 14:31:09 INFO::Fitting model to feature number 74, t143361
2023-03-15 14:31:09 INFO::Fitting model to feature number 75, t2823316
2023-03-15 14:31:09 INFO::Fitting model to feature number 76, t2093857
2023-03-15 14:31:09 INFO::Fitting model to feature number 77, t84030
2023-03-15 14:31:09 INFO::Fitting model to feature number 78, t1464
2023-03-15 14:31:09 INFO::Fitting model to feature number 79, t1297617
2023-03-15 14:31:09 INFO::Fitting model to feature number 80, t2714355
2023-03-15 14:31:09 INFO::Fitting model to feature number 81, t83655
2023-03-15 14:31:09 INFO::Fitting model to feature number 82, t2774055
2023-03-15 14:31:09 INFO::Fitting model to feature number 83, t1270
2023-03-15 14:31:09 INFO::Fitting model to feature number 84, t39485
2023-03-15 14:31:09 INFO::Fitting model to feature number 85, t1583
2023-03-15 14:31:09 INFO::Fitting model to feature number 86, t71999
2023-03-15 14:31:09 INFO::Counting total values for each feature
2023-03-15 14:31:09 INFO::Writing residuals to file maaslin_outputs/seroconv_Malawi_unadjusted/residuals.rds
2023-03-15 14:31:09 INFO::Writing fitted values to file maaslin_outputs/seroconv_Malawi_unadjusted/fitted.rds
2023-03-15 14:31:09 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/seroconv_Malawi_unadjusted/all_results.tsv
2023-03-15 14:31:09 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/seroconv_Malawi_unadjusted/significant_results.tsv
2023-03-15 14:31:09 INFO::Writing heatmap of significant results to file: maaslin_outputs/seroconv_Malawi_unadjusted/heatmap.pdf
[1] "There are no associations to plot!"
[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:31:09 INFO::Writing function arguments to log file
2023-03-15 14:31:10 INFO::Verifying options selected are valid
2023-03-15 14:31:10 INFO::Determining format of input files
2023-03-15 14:31:10 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:31:10 INFO::Formula for fixed effects: expr ~  seroconv + age_at_first_dose + antibiotic_exposure + birth_weight + breastfed_child
2023-03-15 14:31:10 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:31:10 INFO::Total samples in data: 56
2023-03-15 14:31:10 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:31:10 INFO::Total filtered features: 0
2023-03-15 14:31:10 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:31:10 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:31:10 INFO::Filtered feature names from variance filtering:
2023-03-15 14:31:10 INFO::Running selected normalization method: NONE
2023-03-15 14:31:10 INFO::Bypass z-score application to metadata
2023-03-15 14:31:10 INFO::Running selected transform method: AST
2023-03-15 14:31:10 INFO::Running selected analysis method: LM
2023-03-15 14:31:10 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:31:10 INFO::Fitting model to feature number 2, t562
2023-03-15 14:31:10 INFO::Fitting model to feature number 3, t573
2023-03-15 14:31:10 INFO::Fitting model to feature number 4, t817
2023-03-15 14:31:10 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:31:10 INFO::Fitting model to feature number 6, t823
2023-03-15 14:31:10 INFO::Fitting model to feature number 7, t821
2023-03-15 14:31:10 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:31:10 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:31:10 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:31:10 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:31:10 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:31:10 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:31:10 INFO::Fitting model to feature number 14, t550
2023-03-15 14:31:10 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:31:10 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:31:10 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:31:10 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:31:10 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:31:10 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:31:10 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:31:10 INFO::Fitting model to feature number 22, t729
2023-03-15 14:31:10 INFO::Fitting model to feature number 23, t907
2023-03-15 14:31:10 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:31:10 INFO::Fitting model to feature number 25, t853
2023-03-15 14:31:10 INFO::Fitting model to feature number 26, t197
2023-03-15 14:31:10 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:31:10 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:31:10 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:31:10 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:31:10 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:31:10 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:31:10 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:31:10 INFO::Fitting model to feature number 34, t584
2023-03-15 14:31:10 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:31:10 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:31:10 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:31:10 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:31:10 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:31:10 INFO::Fitting model to feature number 40, t624
2023-03-15 14:31:10 INFO::Fitting model to feature number 41, t545
2023-03-15 14:31:10 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:31:10 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:31:10 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:31:10 INFO::Fitting model to feature number 45, t582
2023-03-15 14:31:10 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:31:10 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:31:10 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:31:10 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:31:10 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:31:10 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:31:10 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:31:10 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:31:10 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:31:10 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:31:10 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:31:10 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:31:10 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:31:10 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:31:10 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:31:10 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:31:10 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:31:10 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:31:10 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:31:10 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:31:10 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:31:10 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:31:10 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:31:10 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:31:10 INFO::Fitting model to feature number 70, t287
2023-03-15 14:31:10 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:31:10 INFO::Fitting model to feature number 72, t901
2023-03-15 14:31:10 INFO::Fitting model to feature number 73, t604330
2023-03-15 14:31:10 INFO::Fitting model to feature number 74, t143361
2023-03-15 14:31:10 INFO::Fitting model to feature number 75, t2823316
2023-03-15 14:31:10 INFO::Fitting model to feature number 76, t2093857
2023-03-15 14:31:10 INFO::Fitting model to feature number 77, t84030
2023-03-15 14:31:10 INFO::Fitting model to feature number 78, t1464
2023-03-15 14:31:10 INFO::Fitting model to feature number 79, t1297617
2023-03-15 14:31:10 INFO::Fitting model to feature number 80, t2714355
2023-03-15 14:31:10 INFO::Fitting model to feature number 81, t83655
2023-03-15 14:31:10 INFO::Fitting model to feature number 82, t2774055
2023-03-15 14:31:10 INFO::Fitting model to feature number 83, t1270
2023-03-15 14:31:10 INFO::Fitting model to feature number 84, t39485
2023-03-15 14:31:10 INFO::Fitting model to feature number 85, t1583
2023-03-15 14:31:10 INFO::Fitting model to feature number 86, t71999
2023-03-15 14:31:10 INFO::Counting total values for each feature
2023-03-15 14:31:10 INFO::Writing residuals to file maaslin_outputs/seroconv_Malawi_adjusted/residuals.rds
2023-03-15 14:31:10 INFO::Writing fitted values to file maaslin_outputs/seroconv_Malawi_adjusted/fitted.rds
2023-03-15 14:31:10 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/seroconv_Malawi_adjusted/all_results.tsv
2023-03-15 14:31:10 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/seroconv_Malawi_adjusted/significant_results.tsv
2023-03-15 14:31:10 INFO::Writing heatmap of significant results to file: maaslin_outputs/seroconv_Malawi_adjusted/heatmap.pdf
[1] "There are no associations to plot!"

     country n_tested_fisher n_signif_fisher n_tested_lr n_signif_lr
1        MLW              78               0          78           0
2 IND (neo-)              81              13          81          19
3 IND (neo+)              79               0          79           0
4        IND              80              11          80          16
  n_tested_maaslin n_signif_maaslin
1               86                0
2               86                0
3               85                0
4               85                0

     country n_neg n_equal n_pos total proportion_neg
1        IND    66       1    13    80          82.5%
2 IND (neo+)    51       0    28    79          64.6%
3 IND (neo-)    68       3    10    81            84%
4        MLW    61       0    17    78          78.2%

                       [,1]
IND            9.900480e-12
MLW            2.753823e-08
IND_exposed    3.014039e-04
IND_nonexposed 1.665936e-11

                       [,1]
IND            6.625381e-04
MLW            2.966985e-03
IND_exposed    9.416334e-02
IND_nonexposed 3.846141e-05

     country n_neg n_equal n_pos total proportion_neg
1        IND    57       0    28    85          67.1%
2 IND (neo+)    51       0    34    85            60%
3 IND (neo-)    64       0    22    86          74.4%
4        MLW    54       0    32    86          62.8%

      subset     N_features FDR p<0.2 unadjusted FDR p<0.2 adjusted
1        IND 85 (28 +/57 -)          0 (0 +/0 -)        0 (0 +/0 -)
2 IND (neo+) 85 (34 +/51 -)          0 (0 +/0 -)        0 (0 +/0 -)
3 IND (neo-) 86 (22 +/64 -)          0 (0 +/0 -)        0 (0 +/0 -)
4        MLW 86 (32 +/54 -)          0 (0 +/0 -)        0 (0 +/0 -)

Spearman’s rho matrix of statistical test p values - India

#### Rho values

                                Fisher p       LR p LR (adj) p   Wilcox p
Fisher p                      1.00000000 0.99580905 0.94837785  0.7595205
LR p                          0.99580905 1.00000000 0.95386779  0.7506798
LR (adj) p                    0.94837785 0.95386779 1.00000000  0.7310595
Wilcox p                      0.75952055 0.75067979 0.73105954  1.0000000
Maaslin p                     0.22469447 0.23541960 0.20002344  0.3995312
Maaslin (adj) p               0.21060345 0.22116737 0.22151899  0.3451711
RF rank                       0.06779403 0.06507267 0.04510080 -0.0261369
Inv. abs. Maaslin coef. (adj) 0.09467484 0.10982185 0.05356306  0.1688936
Inv. abs. Prev. diff.         0.97927073 0.97522493 0.93110220  0.7915013
Inv. abs. ean abund. diff.    0.07080684 0.08164557 0.01172058  0.1209798
                                Maaslin p Maaslin (adj) p      RF rank
Fisher p                       0.22469447     0.210603445  0.067794029
LR p                           0.23541960     0.221167370  0.065072668
LR (adj) p                     0.20002344     0.221518987  0.045100797
Wilcox p                       0.39953118     0.345171120 -0.026136896
Maaslin p                      1.00000000     0.946577590 -0.264158462
Maaslin (adj) p                0.94657759     1.000000000 -0.203187998
RF rank                       -0.26415846    -0.203187998  1.000000000
Inv. abs. Maaslin coef. (adj)  0.50267229     0.551851852  0.278152836
Inv. abs. Prev. diff.          0.25872286     0.238501893  0.001254286
Inv. abs. ean abund. diff.     0.05253165     0.002906704  0.300750117
                              Inv. abs. Maaslin coef. (adj)
Fisher p                                         0.09467484
LR p                                             0.10982185
LR (adj) p                                       0.05356306
Wilcox p                                         0.16889358
Maaslin p                                        0.50267229
Maaslin (adj) p                                  0.55185185
RF rank                                          0.27815284
Inv. abs. Maaslin coef. (adj)                    1.00000000
Inv. abs. Prev. diff.                            0.10362512
Inv. abs. ean abund. diff.                       0.67592593
                              Inv. abs. Prev. diff. Inv. abs. ean abund. diff.
Fisher p                                0.979270725                0.070806836
LR p                                    0.975224932                0.081645570
LR (adj) p                              0.931102199                0.011720581
Wilcox p                                0.791501342                0.120979841
Maaslin p                               0.258722858                0.052531646
Maaslin (adj) p                         0.238501893                0.002906704
RF rank                                 0.001254286                0.300750117
Inv. abs. Maaslin coef. (adj)           0.103625122                0.675925926
Inv. abs. Prev. diff.                   1.000000000                0.080731472
Inv. abs. ean abund. diff.              0.080731472                1.000000000

N features with full data across tests: 80

Spearman’s rho matrix of statistical test p values - India (neo+)

#### Rho values

                                 Fisher p        LR p  LR (adj) p    Wilcox p
Fisher p                       1.00000000  0.99011042  0.89144917  0.79239791
LR p                           0.99011042  1.00000000  0.89987829  0.79810127
LR (adj) p                     0.89144917  0.89987829  1.00000000  0.68877799
Wilcox p                       0.79239791  0.79810127  0.68877799  1.00000000
Maaslin p                      0.15984463  0.14681110  0.19055501  0.34629990
Maaslin (adj) p                0.26923125  0.25652386  0.27801850  0.36363194
RF rank                        0.14354937  0.15703505  0.13154820  0.14724927
Inv. abs. Maaslin coef. (adj)  0.07937995  0.10457644  0.05966407  0.02663096
Inv. abs. prev. diff.          0.97250164  0.97814378  0.89622097  0.77910664
Inv. abs. mean abund. diff.   -0.06058617 -0.04759007 -0.08064752 -0.14576436
                                Maaslin p Maaslin (adj) p     RF rank
Fisher p                       0.15984463      0.26923125  0.14354937
LR p                           0.14681110      0.25652386  0.15703505
LR (adj) p                     0.19055501      0.27801850  0.13154820
Wilcox p                       0.34629990      0.36363194  0.14724927
Maaslin p                      1.00000000      0.83851022 -0.04277020
Maaslin (adj) p                0.83851022      1.00000000 -0.03588121
RF rank                       -0.04277020     -0.03588121  1.00000000
Inv. abs. Maaslin coef. (adj)  0.25270204      0.40572055  0.37548685
Inv. abs. prev. diff.          0.14701067      0.25823337  0.11489888
Inv. abs. mean abund. diff.    0.03028238     -0.01815969  0.29810127
                              Inv. abs. Maaslin coef. (adj)
Fisher p                                         0.07937995
LR p                                             0.10457644
LR (adj) p                                       0.05966407
Wilcox p                                         0.02663096
Maaslin p                                        0.25270204
Maaslin (adj) p                                  0.40572055
RF rank                                          0.37548685
Inv. abs. Maaslin coef. (adj)                    1.00000000
Inv. abs. prev. diff.                            0.08139938
Inv. abs. mean abund. diff.                      0.77176241
                              Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p                                 0.97250164                 -0.06058617
LR p                                     0.97814378                 -0.04759007
LR (adj) p                               0.89622097                 -0.08064752
Wilcox p                                 0.77910664                 -0.14576436
Maaslin p                                0.14701067                  0.03028238
Maaslin (adj) p                          0.25823337                 -0.01815969
RF rank                                  0.11489888                  0.29810127
Inv. abs. Maaslin coef. (adj)            0.08139938                  0.77176241
Inv. abs. prev. diff.                    1.00000000                 -0.05604348
Inv. abs. mean abund. diff.             -0.05604348                  1.00000000

N features with full data across tests: 79

                               Fisher p       LR p  LR (adj) p  Wilcox p
Fisher p                      1.0000000 0.98167867 0.914660408 0.8019173
LR p                          0.9816787 1.00000000 0.935325237 0.7855711
LR (adj) p                    0.9146604 0.93532524 1.000000000 0.6639341
Wilcox p                      0.8019173 0.78557112 0.663934056 1.0000000
Maaslin p                     0.3235473 0.30872248 0.255645890 0.4882791
Maaslin (adj) p               0.3867287 0.38144278 0.336427281 0.4946251
RF rank                       0.2339406 0.24870566 0.290063234 0.1787037
Inv. abs. Maaslin coef. (adj) 0.1842545 0.19185058 0.165334237 0.3232159
Inv. abs. prev. diff.         0.9599458 0.96629982 0.889505513 0.8245917
Inv. abs. mean abund. diff.   0.0139305 0.02889632 0.006018552 0.1327695
                                Maaslin p Maaslin (adj) p     RF rank
Fisher p                       0.32354734      0.38672871  0.23394058
LR p                           0.30872248      0.38144278  0.24870566
LR (adj) p                     0.25564589      0.33642728  0.29006323
Wilcox p                       0.48827913      0.49462511  0.17870370
Maaslin p                      1.00000000      0.89769648 -0.07585818
Maaslin (adj) p                0.89769648      1.00000000 -0.05948509
RF rank                       -0.07585818     -0.05948509  1.00000000
Inv. abs. Maaslin coef. (adj)  0.55101626      0.56192412  0.30641373
Inv. abs. prev. diff.          0.31795898      0.36890700  0.17945361
Inv. abs. mean abund. diff.    0.27668404      0.18952230  0.33212699
                              Inv. abs. Maaslin coef. (adj)
Fisher p                                          0.1842545
LR p                                              0.1918506
LR (adj) p                                        0.1653342
Wilcox p                                          0.3232159
Maaslin p                                         0.5510163
Maaslin (adj) p                                   0.5619241
RF rank                                           0.3064137
Inv. abs. Maaslin coef. (adj)                     1.0000000
Inv. abs. prev. diff.                             0.1350026
Inv. abs. mean abund. diff.                       0.8292617
                              Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p                                 0.95994576                 0.013930495
LR p                                     0.96629982                 0.028896317
LR (adj) p                               0.88950551                 0.006018552
Wilcox p                                 0.82459171                 0.132769494
Maaslin p                                0.31795898                 0.276684037
Maaslin (adj) p                          0.36890700                 0.189522299
RF rank                                  0.17945361                 0.332126988
Inv. abs. Maaslin coef. (adj)            0.13500263                 0.829261683
Inv. abs. prev. diff.                    1.00000000                -0.020400788
Inv. abs. mean abund. diff.             -0.02040079                 1.000000000

                               Fisher p      LR p LR (adj) p  Wilcox p
Fisher p                      1.0000000 0.9602776  0.9252675 0.8021623
LR p                          0.9602776 1.0000000  0.9503696 0.8208968
LR (adj) p                    0.9252675 0.9503696  1.0000000 0.7513373
Wilcox p                      0.8021623 0.8208968  0.7513373 1.0000000
Maaslin p                     0.2530975 0.2906879  0.2426814 0.4158753
Maaslin (adj) p               0.2068918 0.2381299  0.1990288 0.3591978
RF rank                       0.3902685 0.3144124  0.2470567 0.4061129
Inv. abs. maaslin coef. (adj) 0.2297600 0.2385851  0.2162015 0.2938454
Inv. abs. prev. diff.         0.9020605 0.9312925  0.8726742 0.7215680
Inv. abs. mean abund. diff.   0.1553084 0.1465074  0.1190076 0.1563879
                              Maaslin p Maaslin (adj) p   RF rank
Fisher p                      0.2530975       0.2068918 0.3902685
LR p                          0.2906879       0.2381299 0.3144124
LR (adj) p                    0.2426814       0.1990288 0.2470567
Wilcox p                      0.4158753       0.3591978 0.4061129
Maaslin p                     1.0000000       0.9414004 0.2986254
Maaslin (adj) p               0.9414004       1.0000000 0.2443759
RF rank                       0.2986254       0.2443759 1.0000000
Inv. abs. maaslin coef. (adj) 0.6282705       0.6832787 0.4292290
Inv. abs. prev. diff.         0.2123405       0.1553436 0.2345776
Inv. abs. mean abund. diff.   0.3399006       0.3425309 0.4847431
                              Inv. abs. maaslin coef. (adj)
Fisher p                                          0.2297600
LR p                                              0.2385851
LR (adj) p                                        0.2162015
Wilcox p                                          0.2938454
Maaslin p                                         0.6282705
Maaslin (adj) p                                   0.6832787
RF rank                                           0.4292290
Inv. abs. maaslin coef. (adj)                     1.0000000
Inv. abs. prev. diff.                             0.1407466
Inv. abs. mean abund. diff.                       0.8596593
                              Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p                                 0.90206049                  0.15530836
LR p                                     0.93129252                  0.14650741
LR (adj) p                               0.87267418                  0.11900757
Wilcox p                                 0.72156801                  0.15638792
Maaslin p                                0.21234047                  0.33990061
Maaslin (adj) p                          0.15534362                  0.34253089
RF rank                                  0.23457759                  0.48474310
Inv. abs. maaslin coef. (adj)            0.14074656                  0.85965933
Inv. abs. prev. diff.                    1.00000000                  0.06296723
Inv. abs. mean abund. diff.              0.06296723                  1.00000000

RV-IgA

[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:32:53 INFO::Writing function arguments to log file
2023-03-15 14:32:53 INFO::Verifying options selected are valid
2023-03-15 14:32:53 INFO::Determining format of input files
2023-03-15 14:32:53 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:32:53 INFO::Formula for fixed effects: expr ~  IgA
2023-03-15 14:32:53 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:32:53 INFO::Total samples in data: 282
2023-03-15 14:32:53 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:32:53 INFO::Total filtered features: 0
2023-03-15 14:32:53 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:32:53 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:32:53 INFO::Filtered feature names from variance filtering:
2023-03-15 14:32:53 INFO::Running selected normalization method: NONE
2023-03-15 14:32:53 INFO::Bypass z-score application to metadata
2023-03-15 14:32:53 INFO::Running selected transform method: AST
2023-03-15 14:32:53 INFO::Running selected analysis method: LM
2023-03-15 14:32:53 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:32:53 INFO::Fitting model to feature number 2, t562
2023-03-15 14:32:53 INFO::Fitting model to feature number 3, t573
2023-03-15 14:32:53 INFO::Fitting model to feature number 4, t817
2023-03-15 14:32:53 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:32:53 INFO::Fitting model to feature number 6, t823
2023-03-15 14:32:53 INFO::Fitting model to feature number 7, t821
2023-03-15 14:32:53 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:32:53 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:32:53 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:32:54 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:32:54 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:32:54 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:32:54 INFO::Fitting model to feature number 14, t550
2023-03-15 14:32:54 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:32:54 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:32:54 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:32:54 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:32:54 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:32:54 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:32:54 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:32:54 INFO::Fitting model to feature number 22, t729
2023-03-15 14:32:54 INFO::Fitting model to feature number 23, t907
2023-03-15 14:32:54 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:32:54 INFO::Fitting model to feature number 25, t853
2023-03-15 14:32:54 INFO::Fitting model to feature number 26, t197
2023-03-15 14:32:54 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:32:54 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:32:54 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:32:54 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:32:54 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:32:54 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:32:54 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:32:54 INFO::Fitting model to feature number 34, t584
2023-03-15 14:32:54 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:32:54 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:32:54 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:32:54 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:32:54 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:32:54 INFO::Fitting model to feature number 40, t624
2023-03-15 14:32:54 INFO::Fitting model to feature number 41, t545
2023-03-15 14:32:54 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:32:54 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:32:54 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:32:54 INFO::Fitting model to feature number 45, t582
2023-03-15 14:32:54 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:32:54 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:32:54 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:32:54 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:32:54 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:32:54 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:32:54 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:32:54 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:32:54 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:32:54 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:32:54 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:32:54 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:32:54 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:32:54 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:32:54 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:32:54 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:32:54 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:32:54 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:32:54 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:32:54 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:32:54 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:32:54 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:32:54 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:32:54 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:32:54 INFO::Fitting model to feature number 70, t287
2023-03-15 14:32:54 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:32:54 INFO::Fitting model to feature number 72, t604330
2023-03-15 14:32:54 INFO::Fitting model to feature number 73, t143361
2023-03-15 14:32:54 INFO::Fitting model to feature number 74, t2823316
2023-03-15 14:32:54 INFO::Fitting model to feature number 75, t2093857
2023-03-15 14:32:54 INFO::Fitting model to feature number 76, t84030
2023-03-15 14:32:54 INFO::Fitting model to feature number 77, t1464
2023-03-15 14:32:54 INFO::Fitting model to feature number 78, t1297617
2023-03-15 14:32:54 INFO::Fitting model to feature number 79, t2714355
2023-03-15 14:32:54 INFO::Fitting model to feature number 80, t83655
2023-03-15 14:32:54 INFO::Fitting model to feature number 81, t2774055
2023-03-15 14:32:54 INFO::Fitting model to feature number 82, t1270
2023-03-15 14:32:54 INFO::Fitting model to feature number 83, t39485
2023-03-15 14:32:54 INFO::Fitting model to feature number 84, t1583
2023-03-15 14:32:54 INFO::Fitting model to feature number 85, t71999
2023-03-15 14:32:54 INFO::Counting total values for each feature
2023-03-15 14:32:54 INFO::Writing residuals to file maaslin_outputs/IgA_India_unadjusted/residuals.rds
2023-03-15 14:32:54 INFO::Writing fitted values to file maaslin_outputs/IgA_India_unadjusted/fitted.rds
2023-03-15 14:32:54 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/IgA_India_unadjusted/all_results.tsv
2023-03-15 14:32:54 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/IgA_India_unadjusted/significant_results.tsv
2023-03-15 14:32:54 INFO::Writing heatmap of significant results to file: maaslin_outputs/IgA_India_unadjusted/heatmap.pdf
[1] "There are no associations to plot!"
[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:32:54 INFO::Writing function arguments to log file
2023-03-15 14:32:54 INFO::Verifying options selected are valid
2023-03-15 14:32:54 INFO::Determining format of input files
2023-03-15 14:32:54 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:32:54 INFO::Formula for fixed effects: expr ~  IgA + age_at_first_dose + antibiotic_exposure + birth_weight + breastfed_child + mode_delivery
2023-03-15 14:32:54 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:32:54 INFO::Total samples in data: 282
2023-03-15 14:32:54 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:32:54 INFO::Total filtered features: 0
2023-03-15 14:32:54 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:32:54 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:32:54 INFO::Filtered feature names from variance filtering:
2023-03-15 14:32:54 INFO::Running selected normalization method: NONE
2023-03-15 14:32:54 INFO::Bypass z-score application to metadata
2023-03-15 14:32:54 INFO::Running selected transform method: AST
2023-03-15 14:32:54 INFO::Running selected analysis method: LM
2023-03-15 14:32:54 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:32:54 INFO::Fitting model to feature number 2, t562
2023-03-15 14:32:54 INFO::Fitting model to feature number 3, t573
2023-03-15 14:32:54 INFO::Fitting model to feature number 4, t817
2023-03-15 14:32:54 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:32:54 INFO::Fitting model to feature number 6, t823
2023-03-15 14:32:54 INFO::Fitting model to feature number 7, t821
2023-03-15 14:32:54 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:32:54 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:32:54 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:32:54 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:32:54 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:32:54 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:32:54 INFO::Fitting model to feature number 14, t550
2023-03-15 14:32:54 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:32:54 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:32:54 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:32:54 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:32:54 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:32:54 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:32:54 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:32:54 INFO::Fitting model to feature number 22, t729
2023-03-15 14:32:54 INFO::Fitting model to feature number 23, t907
2023-03-15 14:32:54 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:32:54 INFO::Fitting model to feature number 25, t853
2023-03-15 14:32:54 INFO::Fitting model to feature number 26, t197
2023-03-15 14:32:54 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:32:54 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:32:54 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:32:54 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:32:54 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:32:54 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:32:54 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:32:54 INFO::Fitting model to feature number 34, t584
2023-03-15 14:32:54 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:32:54 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:32:54 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:32:54 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:32:54 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:32:54 INFO::Fitting model to feature number 40, t624
2023-03-15 14:32:54 INFO::Fitting model to feature number 41, t545
2023-03-15 14:32:54 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:32:54 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:32:54 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:32:54 INFO::Fitting model to feature number 45, t582
2023-03-15 14:32:54 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:32:54 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:32:54 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:32:54 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:32:54 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:32:54 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:32:54 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:32:54 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:32:54 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:32:54 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:32:54 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:32:54 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:32:54 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:32:54 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:32:54 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:32:54 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:32:54 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:32:54 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:32:54 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:32:54 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:32:54 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:32:54 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:32:54 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:32:54 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:32:54 INFO::Fitting model to feature number 70, t287
2023-03-15 14:32:54 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:32:54 INFO::Fitting model to feature number 72, t604330
2023-03-15 14:32:54 INFO::Fitting model to feature number 73, t143361
2023-03-15 14:32:54 INFO::Fitting model to feature number 74, t2823316
2023-03-15 14:32:54 INFO::Fitting model to feature number 75, t2093857
2023-03-15 14:32:54 INFO::Fitting model to feature number 76, t84030
2023-03-15 14:32:54 INFO::Fitting model to feature number 77, t1464
2023-03-15 14:32:54 INFO::Fitting model to feature number 78, t1297617
2023-03-15 14:32:54 INFO::Fitting model to feature number 79, t2714355
2023-03-15 14:32:54 INFO::Fitting model to feature number 80, t83655
2023-03-15 14:32:54 INFO::Fitting model to feature number 81, t2774055
2023-03-15 14:32:54 INFO::Fitting model to feature number 82, t1270
2023-03-15 14:32:54 INFO::Fitting model to feature number 83, t39485
2023-03-15 14:32:54 INFO::Fitting model to feature number 84, t1583
2023-03-15 14:32:54 INFO::Fitting model to feature number 85, t71999
2023-03-15 14:32:54 INFO::Counting total values for each feature
2023-03-15 14:32:55 INFO::Writing residuals to file maaslin_outputs/IgA_India_adjusted/residuals.rds
2023-03-15 14:32:55 INFO::Writing fitted values to file maaslin_outputs/IgA_India_adjusted/fitted.rds
2023-03-15 14:32:55 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/IgA_India_adjusted/all_results.tsv
2023-03-15 14:32:55 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/IgA_India_adjusted/significant_results.tsv
2023-03-15 14:32:55 INFO::Writing heatmap of significant results to file: maaslin_outputs/IgA_India_adjusted/heatmap.pdf

[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:33:40 INFO::Writing function arguments to log file
2023-03-15 14:33:40 INFO::Verifying options selected are valid
2023-03-15 14:33:40 INFO::Determining format of input files
2023-03-15 14:33:40 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:33:40 INFO::Formula for fixed effects: expr ~  IgA
2023-03-15 14:33:40 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:33:40 INFO::Total samples in data: 149
2023-03-15 14:33:40 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:33:40 INFO::Total filtered features: 0
2023-03-15 14:33:40 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:33:40 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:33:40 INFO::Filtered feature names from variance filtering:
2023-03-15 14:33:40 INFO::Running selected normalization method: NONE
2023-03-15 14:33:40 INFO::Bypass z-score application to metadata
2023-03-15 14:33:40 INFO::Running selected transform method: AST
2023-03-15 14:33:40 INFO::Running selected analysis method: LM
2023-03-15 14:33:40 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:33:40 INFO::Fitting model to feature number 2, t562
2023-03-15 14:33:40 INFO::Fitting model to feature number 3, t573
2023-03-15 14:33:40 INFO::Fitting model to feature number 4, t817
2023-03-15 14:33:40 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:33:40 INFO::Fitting model to feature number 6, t823
2023-03-15 14:33:40 INFO::Fitting model to feature number 7, t821
2023-03-15 14:33:40 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:33:40 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:33:40 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:33:40 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:33:40 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:33:40 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:33:40 INFO::Fitting model to feature number 14, t550
2023-03-15 14:33:40 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:33:40 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:33:40 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:33:40 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:33:40 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:33:40 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:33:40 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:33:40 INFO::Fitting model to feature number 22, t729
2023-03-15 14:33:40 INFO::Fitting model to feature number 23, t907
2023-03-15 14:33:40 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:33:40 INFO::Fitting model to feature number 25, t853
2023-03-15 14:33:40 INFO::Fitting model to feature number 26, t197
2023-03-15 14:33:40 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:33:40 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:33:40 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:33:40 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:33:40 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:33:40 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:33:40 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:33:40 INFO::Fitting model to feature number 34, t584
2023-03-15 14:33:40 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:33:40 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:33:40 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:33:40 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:33:40 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:33:40 INFO::Fitting model to feature number 40, t624
2023-03-15 14:33:41 INFO::Fitting model to feature number 41, t545
2023-03-15 14:33:41 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:33:41 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:33:41 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:33:41 INFO::Fitting model to feature number 45, t582
2023-03-15 14:33:41 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:33:41 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:33:41 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:33:41 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:33:41 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:33:41 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:33:41 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:33:41 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:33:41 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:33:41 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:33:41 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:33:41 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:33:41 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:33:41 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:33:41 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:33:41 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:33:41 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:33:41 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:33:41 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:33:41 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:33:41 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:33:41 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:33:41 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:33:41 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:33:41 INFO::Fitting model to feature number 70, t287
2023-03-15 14:33:41 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:33:41 INFO::Fitting model to feature number 72, t604330
2023-03-15 14:33:41 INFO::Fitting model to feature number 73, t143361
2023-03-15 14:33:41 INFO::Fitting model to feature number 74, t2823316
2023-03-15 14:33:41 INFO::Fitting model to feature number 75, t2093857
2023-03-15 14:33:41 INFO::Fitting model to feature number 76, t84030
2023-03-15 14:33:41 INFO::Fitting model to feature number 77, t1464
2023-03-15 14:33:41 INFO::Fitting model to feature number 78, t1297617
2023-03-15 14:33:41 INFO::Fitting model to feature number 79, t2714355
2023-03-15 14:33:41 INFO::Fitting model to feature number 80, t83655
2023-03-15 14:33:41 INFO::Fitting model to feature number 81, t2774055
2023-03-15 14:33:41 INFO::Fitting model to feature number 82, t1270
2023-03-15 14:33:41 INFO::Fitting model to feature number 83, t39485
2023-03-15 14:33:41 INFO::Fitting model to feature number 84, t1583
2023-03-15 14:33:41 INFO::Fitting model to feature number 85, t71999
2023-03-15 14:33:41 INFO::Counting total values for each feature
2023-03-15 14:33:41 INFO::Writing residuals to file maaslin_outputs/IgA_India (exposed)_unadjusted/residuals.rds
2023-03-15 14:33:41 INFO::Writing fitted values to file maaslin_outputs/IgA_India (exposed)_unadjusted/fitted.rds
2023-03-15 14:33:41 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/IgA_India (exposed)_unadjusted/all_results.tsv
2023-03-15 14:33:41 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/IgA_India (exposed)_unadjusted/significant_results.tsv
2023-03-15 14:33:41 INFO::Writing heatmap of significant results to file: maaslin_outputs/IgA_India (exposed)_unadjusted/heatmap.pdf
[1] "There is not enough metadata in the associations to create a heatmap plot. Please review the associations in text output file."
[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:33:41 INFO::Writing function arguments to log file
2023-03-15 14:33:41 INFO::Verifying options selected are valid
2023-03-15 14:33:41 INFO::Determining format of input files
2023-03-15 14:33:41 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:33:41 INFO::Formula for fixed effects: expr ~  IgA + age_at_first_dose + antibiotic_exposure + birth_weight + breastfed_child + mode_delivery
2023-03-15 14:33:41 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:33:41 INFO::Total samples in data: 149
2023-03-15 14:33:41 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:33:41 INFO::Total filtered features: 0
2023-03-15 14:33:41 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:33:41 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:33:41 INFO::Filtered feature names from variance filtering:
2023-03-15 14:33:41 INFO::Running selected normalization method: NONE
2023-03-15 14:33:41 INFO::Bypass z-score application to metadata
2023-03-15 14:33:41 INFO::Running selected transform method: AST
2023-03-15 14:33:41 INFO::Running selected analysis method: LM
2023-03-15 14:33:41 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:33:41 INFO::Fitting model to feature number 2, t562
2023-03-15 14:33:41 INFO::Fitting model to feature number 3, t573
2023-03-15 14:33:41 INFO::Fitting model to feature number 4, t817
2023-03-15 14:33:41 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:33:41 INFO::Fitting model to feature number 6, t823
2023-03-15 14:33:41 INFO::Fitting model to feature number 7, t821
2023-03-15 14:33:41 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:33:41 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:33:41 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:33:41 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:33:41 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:33:41 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:33:41 INFO::Fitting model to feature number 14, t550
2023-03-15 14:33:41 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:33:41 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:33:41 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:33:41 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:33:41 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:33:41 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:33:41 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:33:41 INFO::Fitting model to feature number 22, t729
2023-03-15 14:33:41 INFO::Fitting model to feature number 23, t907
2023-03-15 14:33:41 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:33:41 INFO::Fitting model to feature number 25, t853
2023-03-15 14:33:41 INFO::Fitting model to feature number 26, t197
2023-03-15 14:33:41 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:33:41 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:33:41 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:33:41 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:33:41 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:33:41 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:33:41 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:33:41 INFO::Fitting model to feature number 34, t584
2023-03-15 14:33:41 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:33:41 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:33:41 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:33:41 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:33:41 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:33:41 INFO::Fitting model to feature number 40, t624
2023-03-15 14:33:41 INFO::Fitting model to feature number 41, t545
2023-03-15 14:33:41 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:33:41 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:33:41 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:33:41 INFO::Fitting model to feature number 45, t582
2023-03-15 14:33:41 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:33:41 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:33:41 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:33:41 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:33:41 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:33:41 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:33:41 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:33:41 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:33:41 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:33:42 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:33:42 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:33:42 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:33:42 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:33:42 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:33:42 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:33:42 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:33:42 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:33:42 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:33:42 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:33:42 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:33:42 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:33:42 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:33:42 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:33:42 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:33:42 INFO::Fitting model to feature number 70, t287
2023-03-15 14:33:42 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:33:42 INFO::Fitting model to feature number 72, t604330
2023-03-15 14:33:42 INFO::Fitting model to feature number 73, t143361
2023-03-15 14:33:42 INFO::Fitting model to feature number 74, t2823316
2023-03-15 14:33:42 INFO::Fitting model to feature number 75, t2093857
2023-03-15 14:33:42 INFO::Fitting model to feature number 76, t84030
2023-03-15 14:33:42 INFO::Fitting model to feature number 77, t1464
2023-03-15 14:33:42 INFO::Fitting model to feature number 78, t1297617
2023-03-15 14:33:42 INFO::Fitting model to feature number 79, t2714355
2023-03-15 14:33:42 INFO::Fitting model to feature number 80, t83655
2023-03-15 14:33:42 INFO::Fitting model to feature number 81, t2774055
2023-03-15 14:33:42 INFO::Fitting model to feature number 82, t1270
2023-03-15 14:33:42 INFO::Fitting model to feature number 83, t39485
2023-03-15 14:33:42 INFO::Fitting model to feature number 84, t1583
2023-03-15 14:33:42 INFO::Fitting model to feature number 85, t71999
2023-03-15 14:33:42 INFO::Counting total values for each feature
2023-03-15 14:33:42 INFO::Writing residuals to file maaslin_outputs/IgA_India (exposed)_adjusted/residuals.rds
2023-03-15 14:33:42 INFO::Writing fitted values to file maaslin_outputs/IgA_India (exposed)_adjusted/fitted.rds
2023-03-15 14:33:42 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/IgA_India (exposed)_adjusted/all_results.tsv
2023-03-15 14:33:42 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/IgA_India (exposed)_adjusted/significant_results.tsv
2023-03-15 14:33:42 INFO::Writing heatmap of significant results to file: maaslin_outputs/IgA_India (exposed)_adjusted/heatmap.pdf

[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:34:24 INFO::Writing function arguments to log file
2023-03-15 14:34:24 INFO::Verifying options selected are valid
2023-03-15 14:34:24 INFO::Determining format of input files
2023-03-15 14:34:24 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:34:24 INFO::Formula for fixed effects: expr ~  IgA
2023-03-15 14:34:24 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:34:24 INFO::Total samples in data: 132
2023-03-15 14:34:24 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:34:24 INFO::Total filtered features: 0
2023-03-15 14:34:24 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:34:24 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:34:24 INFO::Filtered feature names from variance filtering:
2023-03-15 14:34:24 INFO::Running selected normalization method: NONE
2023-03-15 14:34:24 INFO::Bypass z-score application to metadata
2023-03-15 14:34:24 INFO::Running selected transform method: AST
2023-03-15 14:34:24 INFO::Running selected analysis method: LM
2023-03-15 14:34:24 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:34:24 INFO::Fitting model to feature number 2, t562
2023-03-15 14:34:24 INFO::Fitting model to feature number 3, t573
2023-03-15 14:34:24 INFO::Fitting model to feature number 4, t817
2023-03-15 14:34:24 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:34:24 INFO::Fitting model to feature number 6, t823
2023-03-15 14:34:24 INFO::Fitting model to feature number 7, t821
2023-03-15 14:34:24 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:34:24 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:34:24 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:34:24 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:34:24 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:34:24 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:34:24 INFO::Fitting model to feature number 14, t550
2023-03-15 14:34:24 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:34:24 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:34:24 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:34:24 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:34:24 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:34:24 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:34:24 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:34:24 INFO::Fitting model to feature number 22, t729
2023-03-15 14:34:24 INFO::Fitting model to feature number 23, t907
2023-03-15 14:34:24 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:34:24 INFO::Fitting model to feature number 25, t853
2023-03-15 14:34:24 INFO::Fitting model to feature number 26, t197
2023-03-15 14:34:24 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:34:24 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:34:24 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:34:24 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:34:24 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:34:24 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:34:24 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:34:24 INFO::Fitting model to feature number 34, t584
2023-03-15 14:34:24 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:34:24 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:34:24 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:34:24 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:34:24 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:34:24 INFO::Fitting model to feature number 40, t624
2023-03-15 14:34:24 INFO::Fitting model to feature number 41, t545
2023-03-15 14:34:24 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:34:24 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:34:24 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:34:24 INFO::Fitting model to feature number 45, t582
2023-03-15 14:34:24 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:34:24 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:34:24 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:34:24 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:34:24 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:34:24 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:34:24 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:34:24 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:34:24 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:34:24 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:34:24 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:34:24 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:34:24 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:34:24 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:34:24 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:34:24 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:34:24 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:34:24 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:34:24 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:34:24 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:34:24 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:34:25 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:34:25 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:34:25 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:34:25 INFO::Fitting model to feature number 70, t287
2023-03-15 14:34:25 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:34:25 INFO::Fitting model to feature number 72, t604330
2023-03-15 14:34:25 INFO::Fitting model to feature number 73, t143361
2023-03-15 14:34:25 INFO::Fitting model to feature number 74, t2823316
2023-03-15 14:34:25 INFO::Fitting model to feature number 75, t2093857
2023-03-15 14:34:25 INFO::Fitting model to feature number 76, t84030
2023-03-15 14:34:25 INFO::Fitting model to feature number 77, t1464
2023-03-15 14:34:25 INFO::Fitting model to feature number 78, t1297617
2023-03-15 14:34:25 INFO::Fitting model to feature number 79, t2714355
2023-03-15 14:34:25 INFO::Fitting model to feature number 80, t83655
2023-03-15 14:34:25 INFO::Fitting model to feature number 81, t2774055
2023-03-15 14:34:25 INFO::Fitting model to feature number 82, t1270
2023-03-15 14:34:25 INFO::Fitting model to feature number 83, t39485
2023-03-15 14:34:25 INFO::Fitting model to feature number 84, t1583
2023-03-15 14:34:25 INFO::Fitting model to feature number 85, t71999
2023-03-15 14:34:25 INFO::Counting total values for each feature
2023-03-15 14:34:25 INFO::Writing residuals to file maaslin_outputs/IgA_India (unexposed)_unadjusted/residuals.rds
2023-03-15 14:34:25 INFO::Writing fitted values to file maaslin_outputs/IgA_India (unexposed)_unadjusted/fitted.rds
2023-03-15 14:34:25 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/IgA_India (unexposed)_unadjusted/all_results.tsv
2023-03-15 14:34:25 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/IgA_India (unexposed)_unadjusted/significant_results.tsv
2023-03-15 14:34:25 INFO::Writing heatmap of significant results to file: maaslin_outputs/IgA_India (unexposed)_unadjusted/heatmap.pdf
[1] "There are no associations to plot!"
[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:34:25 INFO::Writing function arguments to log file
2023-03-15 14:34:25 INFO::Verifying options selected are valid
2023-03-15 14:34:25 INFO::Determining format of input files
2023-03-15 14:34:25 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:34:25 INFO::Formula for fixed effects: expr ~  IgA + age_at_first_dose + antibiotic_exposure + birth_weight + breastfed_child + mode_delivery
2023-03-15 14:34:25 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:34:25 INFO::Total samples in data: 132
2023-03-15 14:34:25 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:34:25 INFO::Total filtered features: 0
2023-03-15 14:34:25 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:34:25 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:34:25 INFO::Filtered feature names from variance filtering:
2023-03-15 14:34:25 INFO::Running selected normalization method: NONE
2023-03-15 14:34:25 INFO::Bypass z-score application to metadata
2023-03-15 14:34:25 INFO::Running selected transform method: AST
2023-03-15 14:34:25 INFO::Running selected analysis method: LM
2023-03-15 14:34:25 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:34:25 INFO::Fitting model to feature number 2, t562
2023-03-15 14:34:25 INFO::Fitting model to feature number 3, t573
2023-03-15 14:34:25 INFO::Fitting model to feature number 4, t817
2023-03-15 14:34:25 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:34:25 INFO::Fitting model to feature number 6, t823
2023-03-15 14:34:25 INFO::Fitting model to feature number 7, t821
2023-03-15 14:34:25 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:34:25 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:34:25 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:34:25 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:34:25 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:34:25 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:34:25 INFO::Fitting model to feature number 14, t550
2023-03-15 14:34:25 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:34:25 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:34:25 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:34:25 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:34:25 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:34:25 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:34:25 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:34:25 INFO::Fitting model to feature number 22, t729
2023-03-15 14:34:25 INFO::Fitting model to feature number 23, t907
2023-03-15 14:34:25 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:34:25 INFO::Fitting model to feature number 25, t853
2023-03-15 14:34:25 INFO::Fitting model to feature number 26, t197
2023-03-15 14:34:25 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:34:25 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:34:25 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:34:25 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:34:25 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:34:25 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:34:25 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:34:25 INFO::Fitting model to feature number 34, t584
2023-03-15 14:34:25 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:34:25 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:34:25 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:34:25 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:34:25 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:34:25 INFO::Fitting model to feature number 40, t624
2023-03-15 14:34:25 INFO::Fitting model to feature number 41, t545
2023-03-15 14:34:25 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:34:25 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:34:25 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:34:25 INFO::Fitting model to feature number 45, t582
2023-03-15 14:34:25 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:34:25 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:34:25 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:34:25 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:34:25 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:34:25 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:34:25 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:34:25 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:34:25 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:34:25 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:34:25 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:34:25 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:34:25 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:34:25 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:34:25 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:34:25 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:34:25 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:34:25 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:34:25 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:34:25 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:34:25 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:34:25 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:34:25 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:34:25 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:34:25 INFO::Fitting model to feature number 70, t287
2023-03-15 14:34:25 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:34:25 INFO::Fitting model to feature number 72, t604330
2023-03-15 14:34:25 INFO::Fitting model to feature number 73, t143361
2023-03-15 14:34:25 INFO::Fitting model to feature number 74, t2823316
2023-03-15 14:34:25 INFO::Fitting model to feature number 75, t2093857
2023-03-15 14:34:25 INFO::Fitting model to feature number 76, t84030
2023-03-15 14:34:25 INFO::Fitting model to feature number 77, t1464
2023-03-15 14:34:25 INFO::Fitting model to feature number 78, t1297617
2023-03-15 14:34:25 INFO::Fitting model to feature number 79, t2714355
2023-03-15 14:34:25 INFO::Fitting model to feature number 80, t83655
2023-03-15 14:34:25 INFO::Fitting model to feature number 81, t2774055
2023-03-15 14:34:25 INFO::Fitting model to feature number 82, t1270
2023-03-15 14:34:25 INFO::Fitting model to feature number 83, t39485
2023-03-15 14:34:25 INFO::Fitting model to feature number 84, t1583
2023-03-15 14:34:26 INFO::Fitting model to feature number 85, t71999
2023-03-15 14:34:26 INFO::Counting total values for each feature
2023-03-15 14:34:26 INFO::Writing residuals to file maaslin_outputs/IgA_India (unexposed)_adjusted/residuals.rds
2023-03-15 14:34:26 INFO::Writing fitted values to file maaslin_outputs/IgA_India (unexposed)_adjusted/fitted.rds
2023-03-15 14:34:26 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/IgA_India (unexposed)_adjusted/all_results.tsv
2023-03-15 14:34:26 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/IgA_India (unexposed)_adjusted/significant_results.tsv
2023-03-15 14:34:26 INFO::Writing heatmap of significant results to file: maaslin_outputs/IgA_India (unexposed)_adjusted/heatmap.pdf

[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:34:41 INFO::Writing function arguments to log file
2023-03-15 14:34:41 INFO::Verifying options selected are valid
2023-03-15 14:34:41 INFO::Determining format of input files
2023-03-15 14:34:41 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:34:41 INFO::Formula for fixed effects: expr ~  IgA
2023-03-15 14:34:41 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:34:41 INFO::Total samples in data: 56
2023-03-15 14:34:41 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:34:41 INFO::Total filtered features: 0
2023-03-15 14:34:42 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:34:42 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:34:42 INFO::Filtered feature names from variance filtering:
2023-03-15 14:34:42 INFO::Running selected normalization method: NONE
2023-03-15 14:34:42 INFO::Bypass z-score application to metadata
2023-03-15 14:34:42 INFO::Running selected transform method: AST
2023-03-15 14:34:42 INFO::Running selected analysis method: LM
2023-03-15 14:34:42 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:34:42 INFO::Fitting model to feature number 2, t562
2023-03-15 14:34:42 INFO::Fitting model to feature number 3, t573
2023-03-15 14:34:42 INFO::Fitting model to feature number 4, t817
2023-03-15 14:34:42 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:34:42 INFO::Fitting model to feature number 6, t823
2023-03-15 14:34:42 INFO::Fitting model to feature number 7, t821
2023-03-15 14:34:42 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:34:42 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:34:42 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:34:42 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:34:42 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:34:42 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:34:42 INFO::Fitting model to feature number 14, t550
2023-03-15 14:34:42 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:34:42 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:34:42 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:34:42 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:34:42 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:34:42 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:34:42 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:34:42 INFO::Fitting model to feature number 22, t729
2023-03-15 14:34:42 INFO::Fitting model to feature number 23, t907
2023-03-15 14:34:42 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:34:42 INFO::Fitting model to feature number 25, t853
2023-03-15 14:34:42 INFO::Fitting model to feature number 26, t197
2023-03-15 14:34:42 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:34:42 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:34:42 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:34:42 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:34:42 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:34:42 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:34:42 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:34:42 INFO::Fitting model to feature number 34, t584
2023-03-15 14:34:42 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:34:42 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:34:42 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:34:42 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:34:42 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:34:42 INFO::Fitting model to feature number 40, t624
2023-03-15 14:34:42 INFO::Fitting model to feature number 41, t545
2023-03-15 14:34:42 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:34:42 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:34:42 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:34:42 INFO::Fitting model to feature number 45, t582
2023-03-15 14:34:42 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:34:42 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:34:42 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:34:42 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:34:42 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:34:42 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:34:42 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:34:42 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:34:42 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:34:42 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:34:42 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:34:42 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:34:42 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:34:42 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:34:42 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:34:42 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:34:42 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:34:42 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:34:42 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:34:42 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:34:42 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:34:42 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:34:42 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:34:42 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:34:42 INFO::Fitting model to feature number 70, t287
2023-03-15 14:34:42 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:34:42 INFO::Fitting model to feature number 72, t901
2023-03-15 14:34:42 INFO::Fitting model to feature number 73, t604330
2023-03-15 14:34:42 INFO::Fitting model to feature number 74, t143361
2023-03-15 14:34:42 INFO::Fitting model to feature number 75, t2823316
2023-03-15 14:34:42 INFO::Fitting model to feature number 76, t2093857
2023-03-15 14:34:42 INFO::Fitting model to feature number 77, t84030
2023-03-15 14:34:42 INFO::Fitting model to feature number 78, t1464
2023-03-15 14:34:42 INFO::Fitting model to feature number 79, t1297617
2023-03-15 14:34:42 INFO::Fitting model to feature number 80, t2714355
2023-03-15 14:34:42 INFO::Fitting model to feature number 81, t83655
2023-03-15 14:34:42 INFO::Fitting model to feature number 82, t2774055
2023-03-15 14:34:42 INFO::Fitting model to feature number 83, t1270
2023-03-15 14:34:42 INFO::Fitting model to feature number 84, t39485
2023-03-15 14:34:42 INFO::Fitting model to feature number 85, t1583
2023-03-15 14:34:42 INFO::Fitting model to feature number 86, t71999
2023-03-15 14:34:42 INFO::Counting total values for each feature
2023-03-15 14:34:42 INFO::Writing residuals to file maaslin_outputs/IgA_Malawi_unadjusted/residuals.rds
2023-03-15 14:34:42 INFO::Writing fitted values to file maaslin_outputs/IgA_Malawi_unadjusted/fitted.rds
2023-03-15 14:34:42 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/IgA_Malawi_unadjusted/all_results.tsv
2023-03-15 14:34:42 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/IgA_Malawi_unadjusted/significant_results.tsv
2023-03-15 14:34:42 INFO::Writing heatmap of significant results to file: maaslin_outputs/IgA_Malawi_unadjusted/heatmap.pdf
[1] "There are no associations to plot!"
[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:34:42 INFO::Writing function arguments to log file
2023-03-15 14:34:42 INFO::Verifying options selected are valid
2023-03-15 14:34:42 INFO::Determining format of input files
2023-03-15 14:34:42 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:34:42 INFO::Formula for fixed effects: expr ~  IgA + age_at_first_dose + antibiotic_exposure + birth_weight + breastfed_child
2023-03-15 14:34:42 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:34:42 INFO::Total samples in data: 56
2023-03-15 14:34:42 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:34:42 INFO::Total filtered features: 0
2023-03-15 14:34:42 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:34:42 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:34:42 INFO::Filtered feature names from variance filtering:
2023-03-15 14:34:42 INFO::Running selected normalization method: NONE
2023-03-15 14:34:42 INFO::Bypass z-score application to metadata
2023-03-15 14:34:42 INFO::Running selected transform method: AST
2023-03-15 14:34:42 INFO::Running selected analysis method: LM
2023-03-15 14:34:42 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:34:42 INFO::Fitting model to feature number 2, t562
2023-03-15 14:34:42 INFO::Fitting model to feature number 3, t573
2023-03-15 14:34:42 INFO::Fitting model to feature number 4, t817
2023-03-15 14:34:42 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:34:42 INFO::Fitting model to feature number 6, t823
2023-03-15 14:34:42 INFO::Fitting model to feature number 7, t821
2023-03-15 14:34:42 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:34:42 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:34:42 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:34:42 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:34:42 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:34:42 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:34:42 INFO::Fitting model to feature number 14, t550
2023-03-15 14:34:42 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:34:42 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:34:42 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:34:42 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:34:42 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:34:42 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:34:42 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:34:42 INFO::Fitting model to feature number 22, t729
2023-03-15 14:34:42 INFO::Fitting model to feature number 23, t907
2023-03-15 14:34:42 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:34:42 INFO::Fitting model to feature number 25, t853
2023-03-15 14:34:42 INFO::Fitting model to feature number 26, t197
2023-03-15 14:34:42 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:34:42 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:34:42 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:34:42 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:34:42 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:34:42 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:34:42 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:34:42 INFO::Fitting model to feature number 34, t584
2023-03-15 14:34:42 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:34:42 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:34:42 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:34:42 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:34:42 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:34:42 INFO::Fitting model to feature number 40, t624
2023-03-15 14:34:42 INFO::Fitting model to feature number 41, t545
2023-03-15 14:34:42 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:34:42 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:34:42 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:34:42 INFO::Fitting model to feature number 45, t582
2023-03-15 14:34:42 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:34:42 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:34:42 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:34:42 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:34:42 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:34:42 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:34:42 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:34:42 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:34:42 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:34:42 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:34:42 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:34:42 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:34:42 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:34:42 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:34:42 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:34:42 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:34:42 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:34:42 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:34:42 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:34:42 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:34:42 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:34:42 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:34:42 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:34:42 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:34:43 INFO::Fitting model to feature number 70, t287
2023-03-15 14:34:43 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:34:43 INFO::Fitting model to feature number 72, t901
2023-03-15 14:34:43 INFO::Fitting model to feature number 73, t604330
2023-03-15 14:34:43 INFO::Fitting model to feature number 74, t143361
2023-03-15 14:34:43 INFO::Fitting model to feature number 75, t2823316
2023-03-15 14:34:43 INFO::Fitting model to feature number 76, t2093857
2023-03-15 14:34:43 INFO::Fitting model to feature number 77, t84030
2023-03-15 14:34:43 INFO::Fitting model to feature number 78, t1464
2023-03-15 14:34:43 INFO::Fitting model to feature number 79, t1297617
2023-03-15 14:34:43 INFO::Fitting model to feature number 80, t2714355
2023-03-15 14:34:43 INFO::Fitting model to feature number 81, t83655
2023-03-15 14:34:43 INFO::Fitting model to feature number 82, t2774055
2023-03-15 14:34:43 INFO::Fitting model to feature number 83, t1270
2023-03-15 14:34:43 INFO::Fitting model to feature number 84, t39485
2023-03-15 14:34:43 INFO::Fitting model to feature number 85, t1583
2023-03-15 14:34:43 INFO::Fitting model to feature number 86, t71999
2023-03-15 14:34:43 INFO::Counting total values for each feature
2023-03-15 14:34:43 INFO::Writing residuals to file maaslin_outputs/IgA_Malawi_adjusted/residuals.rds
2023-03-15 14:34:43 INFO::Writing fitted values to file maaslin_outputs/IgA_Malawi_adjusted/fitted.rds
2023-03-15 14:34:43 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/IgA_Malawi_adjusted/all_results.tsv
2023-03-15 14:34:43 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/IgA_Malawi_adjusted/significant_results.tsv
2023-03-15 14:34:43 INFO::Writing heatmap of significant results to file: maaslin_outputs/IgA_Malawi_adjusted/heatmap.pdf
[1] "There are no associations to plot!"

     country n_tested_wilcox n_signif_wilcox n_tested_lr n_signif_lr
1        MLW              76               0          76           0
2 IND (neo-)              80               7          80           0
3 IND (neo+)              79               0          79           0
4        IND              80               0          80           0
  n_tested_maaslin n_signif_maaslin
1               86                0
2               85                0
3               85                0
4               85                0

     country n_neg n_equal n_pos total proportion_neg
1        IND    60       0    20    80            75%
2 IND (neo+)    39       0    40    79          49.4%
3 IND (neo-)    66       0    14    80          82.5%
4        MLW    52       0    24    76          68.4%

                       [,1]
IND            2.566686e-06
MLW            5.251126e-02
IND_exposed    7.899733e-01
IND_nonexposed 2.000614e-09

                      [,1]
IND            0.485990367
MLW            0.022478811
IND_exposed    0.012503548
IND_nonexposed 0.002463425

     country n_neg n_equal n_pos total proportion_neg
1        IND    51       0    34    85            60%
2 IND (neo+)    32       0    53    85          37.6%
3 IND (neo-)    58       0    27    85          68.2%
4        MLW    48       0    38    86          55.8%

      subset     N_features FDR p<0.2 unadjusted FDR p<0.2 adjusted
1        IND 85 (34 +/51 -)          0 (0 +/0 -)        0 (0 +/0 -)
2 IND (neo+) 85 (53 +/32 -)          2 (0 +/2 -)        0 (0 +/0 -)
3 IND (neo-) 85 (27 +/58 -)          0 (0 +/0 -)        0 (0 +/0 -)
4        MLW 86 (38 +/48 -)          0 (0 +/0 -)        0 (0 +/0 -)

                              Spearman p      LR p LR (adj) p  Wilcox p
Spearman p                     1.0000000 0.2265588 0.18246601 0.7834505
LR p                           0.2265588 1.0000000 0.90604782 0.1641819
LR (adj) p                     0.1824660 0.9060478 1.00000000 0.1158228
Wilcox p                       0.7834505 0.1641819 0.11582278 1.0000000
Maaslin p                      0.2461088 0.1179794 0.08047351 0.1316456
Maaslin (adj) p                0.3038209 0.1816221 0.14939053 0.1946789
RF rank                        0.4175574 0.1916315 0.21383029 0.3281763
Inv. abs. maaslin coef. (adj)  0.2245898 0.1248242 0.05757150 0.1962729
Inv. abs. GMR-1                0.6635490 0.2298406 0.18572433 0.9394749
                               Maaslin p Maaslin (adj) p   RF rank
Spearman p                    0.24610877       0.3038209 0.4175574
LR p                          0.11797937       0.1816221 0.1916315
LR (adj) p                    0.08047351       0.1493905 0.2138303
Wilcox p                      0.13164557       0.1946789 0.3281763
Maaslin p                     1.00000000       0.8443038 0.1076887
Maaslin (adj) p               0.84430380       1.0000000 0.2127286
RF rank                       0.10768870       0.2127286 1.0000000
Inv. abs. maaslin coef. (adj) 0.52913737       0.6086263 0.1999531
Inv. abs. GMR-1               0.16432255       0.2121660 0.2888186
                              Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p                                        0.2245898       0.6635490
LR p                                              0.1248242       0.2298406
LR (adj) p                                        0.0575715       0.1857243
Wilcox p                                          0.1962729       0.9394749
Maaslin p                                         0.5291374       0.1643226
Maaslin (adj) p                                   0.6086263       0.2121660
RF rank                                           0.1999531       0.2888186
Inv. abs. maaslin coef. (adj)                     1.0000000       0.2362869
Inv. abs. GMR-1                                   0.2362869       1.0000000

                              Spearman p         LR p   LR (adj) p     Wilcox p
Spearman p                     1.0000000  0.257960078  0.119668939  0.600721767
LR p                           0.2579601  1.000000000  0.881475170  0.239205448
LR (adj) p                     0.1196689  0.881475170  1.000000000  0.215714555
Wilcox p                       0.6007218  0.239205448  0.215714555  1.000000000
Maaslin p                      0.4225901  0.127507303  0.086538462  0.105611646
Maaslin (adj) p                0.1953749 -0.046421616 -0.009177215  0.024501123
RF rank                        0.1603944 -0.050365141 -0.091553067 -0.009116414
Inv. abs. maaslin coef. (adj)  0.1132668  0.002702045 -0.042502434  0.010552645
Inv. abs. GMR-1                0.5114167  0.319328140  0.290701071  0.866485312
                               Maaslin p Maaslin (adj) p      RF rank
Spearman p                    0.42259007     0.195374878  0.160394352
LR p                          0.12750730    -0.046421616 -0.050365141
LR (adj) p                    0.08653846    -0.009177215 -0.091553067
Wilcox p                      0.10561165     0.024501123 -0.009116414
Maaslin p                     1.00000000     0.743695229  0.246518987
Maaslin (adj) p               0.74369523     1.000000000  0.267478092
RF rank                       0.24651899     0.267478092  1.000000000
Inv. abs. maaslin coef. (adj) 0.54418208     0.697736125  0.319279455
Inv. abs. GMR-1               0.02877313    -0.034566699  0.026484907
                              Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p                                      0.113266796      0.51141675
LR p                                            0.002702045      0.31932814
LR (adj) p                                     -0.042502434      0.29070107
Wilcox p                                        0.010552645      0.86648531
Maaslin p                                       0.544182084      0.02877313
Maaslin (adj) p                                 0.697736125     -0.03456670
RF rank                                         0.319279455      0.02648491
Inv. abs. maaslin coef. (adj)                   1.000000000     -0.08286271
Inv. abs. GMR-1                                -0.082862707      1.00000000

                              Spearman p       LR p  LR (adj) p   Wilcox p
Spearman p                     1.0000000 0.31293952  0.16249414 0.74357712
LR p                           0.3129395 1.00000000  0.89430380 0.50316456
LR (adj) p                     0.1624941 0.89430380  1.00000000 0.43741210
Wilcox p                       0.7435771 0.50316456  0.43741210 1.00000000
Maaslin p                      0.4250117 0.15935302  0.05630567 0.28401313
Maaslin (adj) p                0.3564463 0.11704173  0.02606657 0.20759494
RF rank                        0.2855134 0.06347867 -0.07301922 0.24714018
Inv. abs. maaslin coef. (adj)  0.2320206 0.04735115 -0.02386310 0.08443507
Inv. abs. GMR-1                0.6818331 0.61150961  0.54714018 0.94275668
                               Maaslin p Maaslin (adj) p     RF rank
Spearman p                    0.42501172      0.35644632  0.28551336
LR p                          0.15935302      0.11704173  0.06347867
LR (adj) p                    0.05630567      0.02606657 -0.07301922
Wilcox p                      0.28401313      0.20759494  0.24714018
Maaslin p                     1.00000000      0.86371308  0.31387717
Maaslin (adj) p               0.86371308      1.00000000  0.22154243
RF rank                       0.31387717      0.22154243  1.00000000
Inv. abs. maaslin coef. (adj) 0.50761838      0.56007970  0.09784341
Inv. abs. GMR-1               0.28799812      0.22123769  0.22053446
                              Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p                                       0.23202063       0.6818331
LR p                                             0.04735115       0.6115096
LR (adj) p                                      -0.02386310       0.5471402
Wilcox p                                         0.08443507       0.9427567
Maaslin p                                        0.50761838       0.2879981
Maaslin (adj) p                                  0.56007970       0.2212377
RF rank                                          0.09784341       0.2205345
Inv. abs. maaslin coef. (adj)                    1.00000000       0.1061650
Inv. abs. GMR-1                                  0.10616503       1.0000000

                              Spearman p       LR p LR (adj) p   Wilcox p
Spearman p                     1.0000000 0.12924129 0.27163363 0.66570517
LR p                           0.1292413 1.00000000 0.70944634 0.07275511
LR (adj) p                     0.2716336 0.70944634 1.00000000 0.30706977
Wilcox p                       0.6657052 0.07275511 0.30706977 1.00000000
Maaslin p                      0.2942994 0.14958305 0.04352700 0.22130021
Maaslin (adj) p                0.2939986 0.11849624 0.05883800 0.26223009
RF rank                        0.3906220 0.10900889 0.15234450 0.34726143
Inv. abs. maaslin coef. (adj)  0.2499248 0.13375256 0.09006152 0.19862063
Inv. abs. GMR-1                0.6932878 0.23852358 0.47524265 0.81399053
                              Maaslin p Maaslin (adj) p   RF rank
Spearman p                    0.2942994       0.2939986 0.3906220
LR p                          0.1495830       0.1184962 0.1090089
LR (adj) p                    0.0435270       0.0588380 0.1523445
Wilcox p                      0.2213002       0.2622301 0.3472614
Maaslin p                     1.0000000       0.9521531 0.2874641
Maaslin (adj) p               0.9521531       1.0000000 0.2969241
RF rank                       0.2874641       0.2969241 1.0000000
Inv. abs. maaslin coef. (adj) 0.6011483       0.6673958 0.1475871
Inv. abs. GMR-1               0.1879152       0.1805058 0.2551470
                              Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p                                       0.24992481       0.6932878
LR p                                             0.13375256       0.2385236
LR (adj) p                                       0.09006152       0.4752427
Wilcox p                                         0.19862063       0.8139905
Maaslin p                                        0.60114833       0.1879152
Maaslin (adj) p                                  0.66739576       0.1805058
RF rank                                          0.14758715       0.2551470
Inv. abs. maaslin coef. (adj)                    1.00000000       0.1616951
Inv. abs. GMR-1                                  0.16169515       1.0000000

Dose 1 shedding

[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:35:01 INFO::Writing function arguments to log file
2023-03-15 14:35:01 INFO::Verifying options selected are valid
2023-03-15 14:35:01 INFO::Determining format of input files
2023-03-15 14:35:01 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:35:01 INFO::Formula for fixed effects: expr ~  dose1_shedding
2023-03-15 14:35:01 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:35:01 INFO::Total samples in data: 281
2023-03-15 14:35:01 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:35:01 INFO::Total filtered features: 0
2023-03-15 14:35:01 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:35:01 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:35:01 INFO::Filtered feature names from variance filtering:
2023-03-15 14:35:01 INFO::Running selected normalization method: NONE
2023-03-15 14:35:01 INFO::Bypass z-score application to metadata
2023-03-15 14:35:01 INFO::Running selected transform method: AST
2023-03-15 14:35:01 INFO::Running selected analysis method: LM
2023-03-15 14:35:01 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:35:01 INFO::Fitting model to feature number 2, t562
2023-03-15 14:35:01 INFO::Fitting model to feature number 3, t573
2023-03-15 14:35:01 INFO::Fitting model to feature number 4, t817
2023-03-15 14:35:01 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:35:01 INFO::Fitting model to feature number 6, t823
2023-03-15 14:35:01 INFO::Fitting model to feature number 7, t821
2023-03-15 14:35:01 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:35:01 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:35:01 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:35:01 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:35:01 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:35:01 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:35:01 INFO::Fitting model to feature number 14, t550
2023-03-15 14:35:01 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:35:01 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:35:01 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:35:01 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:35:01 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:35:01 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:35:01 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:35:01 INFO::Fitting model to feature number 22, t729
2023-03-15 14:35:01 INFO::Fitting model to feature number 23, t907
2023-03-15 14:35:01 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:35:01 INFO::Fitting model to feature number 25, t853
2023-03-15 14:35:01 INFO::Fitting model to feature number 26, t197
2023-03-15 14:35:01 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:35:01 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:35:01 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:35:01 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:35:01 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:35:01 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:35:01 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:35:01 INFO::Fitting model to feature number 34, t584
2023-03-15 14:35:01 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:35:01 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:35:01 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:35:01 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:35:01 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:35:01 INFO::Fitting model to feature number 40, t624
2023-03-15 14:35:01 INFO::Fitting model to feature number 41, t545
2023-03-15 14:35:01 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:35:01 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:35:01 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:35:01 INFO::Fitting model to feature number 45, t582
2023-03-15 14:35:01 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:35:01 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:35:01 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:35:01 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:35:01 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:35:01 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:35:01 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:35:01 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:35:01 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:35:01 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:35:01 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:35:01 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:35:01 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:35:01 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:35:01 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:35:01 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:35:01 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:35:01 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:35:01 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:35:01 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:35:01 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:35:01 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:35:01 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:35:02 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:35:02 INFO::Fitting model to feature number 70, t287
2023-03-15 14:35:02 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:35:02 INFO::Fitting model to feature number 72, t901
2023-03-15 14:35:02 INFO::Fitting model to feature number 73, t604330
2023-03-15 14:35:02 INFO::Fitting model to feature number 74, t143361
2023-03-15 14:35:02 INFO::Fitting model to feature number 75, t2823316
2023-03-15 14:35:02 INFO::Fitting model to feature number 76, t2093857
2023-03-15 14:35:02 INFO::Fitting model to feature number 77, t84030
2023-03-15 14:35:02 INFO::Fitting model to feature number 78, t1464
2023-03-15 14:35:02 INFO::Fitting model to feature number 79, t1297617
2023-03-15 14:35:02 INFO::Fitting model to feature number 80, t2714355
2023-03-15 14:35:02 INFO::Fitting model to feature number 81, t83655
2023-03-15 14:35:02 INFO::Fitting model to feature number 82, t2774055
2023-03-15 14:35:02 INFO::Fitting model to feature number 83, t1270
2023-03-15 14:35:02 INFO::Fitting model to feature number 84, t39485
2023-03-15 14:35:02 INFO::Fitting model to feature number 85, t1583
2023-03-15 14:35:02 INFO::Fitting model to feature number 86, t71999
2023-03-15 14:35:02 INFO::Counting total values for each feature
2023-03-15 14:35:02 INFO::Writing residuals to file maaslin_outputs/dose1_shedding_India_unadjusted/residuals.rds
2023-03-15 14:35:02 INFO::Writing fitted values to file maaslin_outputs/dose1_shedding_India_unadjusted/fitted.rds
2023-03-15 14:35:02 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_India_unadjusted/all_results.tsv
2023-03-15 14:35:02 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_India_unadjusted/significant_results.tsv
2023-03-15 14:35:02 INFO::Writing heatmap of significant results to file: maaslin_outputs/dose1_shedding_India_unadjusted/heatmap.pdf
[1] "There are no associations to plot!"
[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:35:02 INFO::Writing function arguments to log file
2023-03-15 14:35:02 INFO::Verifying options selected are valid
2023-03-15 14:35:02 INFO::Determining format of input files
2023-03-15 14:35:02 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:35:02 INFO::Formula for fixed effects: expr ~  dose1_shedding + age_at_first_dose + antibiotic_exposure + birth_weight + breastfed_child + mode_delivery
2023-03-15 14:35:02 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:35:02 INFO::Total samples in data: 281
2023-03-15 14:35:02 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:35:02 INFO::Total filtered features: 0
2023-03-15 14:35:02 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:35:02 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:35:02 INFO::Filtered feature names from variance filtering:
2023-03-15 14:35:02 INFO::Running selected normalization method: NONE
2023-03-15 14:35:02 INFO::Bypass z-score application to metadata
2023-03-15 14:35:02 INFO::Running selected transform method: AST
2023-03-15 14:35:02 INFO::Running selected analysis method: LM
2023-03-15 14:35:02 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:35:02 INFO::Fitting model to feature number 2, t562
2023-03-15 14:35:02 INFO::Fitting model to feature number 3, t573
2023-03-15 14:35:02 INFO::Fitting model to feature number 4, t817
2023-03-15 14:35:02 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:35:02 INFO::Fitting model to feature number 6, t823
2023-03-15 14:35:02 INFO::Fitting model to feature number 7, t821
2023-03-15 14:35:02 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:35:02 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:35:02 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:35:02 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:35:02 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:35:02 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:35:02 INFO::Fitting model to feature number 14, t550
2023-03-15 14:35:02 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:35:02 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:35:02 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:35:02 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:35:02 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:35:02 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:35:02 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:35:02 INFO::Fitting model to feature number 22, t729
2023-03-15 14:35:02 INFO::Fitting model to feature number 23, t907
2023-03-15 14:35:02 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:35:02 INFO::Fitting model to feature number 25, t853
2023-03-15 14:35:02 INFO::Fitting model to feature number 26, t197
2023-03-15 14:35:02 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:35:02 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:35:02 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:35:02 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:35:02 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:35:02 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:35:02 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:35:02 INFO::Fitting model to feature number 34, t584
2023-03-15 14:35:02 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:35:02 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:35:02 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:35:02 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:35:02 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:35:02 INFO::Fitting model to feature number 40, t624
2023-03-15 14:35:02 INFO::Fitting model to feature number 41, t545
2023-03-15 14:35:02 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:35:02 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:35:02 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:35:02 INFO::Fitting model to feature number 45, t582
2023-03-15 14:35:02 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:35:02 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:35:02 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:35:02 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:35:02 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:35:02 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:35:02 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:35:02 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:35:02 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:35:02 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:35:02 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:35:02 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:35:02 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:35:03 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:35:03 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:35:03 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:35:03 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:35:03 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:35:03 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:35:03 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:35:03 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:35:03 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:35:03 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:35:03 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:35:03 INFO::Fitting model to feature number 70, t287
2023-03-15 14:35:03 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:35:03 INFO::Fitting model to feature number 72, t901
2023-03-15 14:35:03 INFO::Fitting model to feature number 73, t604330
2023-03-15 14:35:03 INFO::Fitting model to feature number 74, t143361
2023-03-15 14:35:03 INFO::Fitting model to feature number 75, t2823316
2023-03-15 14:35:03 INFO::Fitting model to feature number 76, t2093857
2023-03-15 14:35:03 INFO::Fitting model to feature number 77, t84030
2023-03-15 14:35:03 INFO::Fitting model to feature number 78, t1464
2023-03-15 14:35:03 INFO::Fitting model to feature number 79, t1297617
2023-03-15 14:35:03 INFO::Fitting model to feature number 80, t2714355
2023-03-15 14:35:03 INFO::Fitting model to feature number 81, t83655
2023-03-15 14:35:03 INFO::Fitting model to feature number 82, t2774055
2023-03-15 14:35:03 INFO::Fitting model to feature number 83, t1270
2023-03-15 14:35:03 INFO::Fitting model to feature number 84, t39485
2023-03-15 14:35:03 INFO::Fitting model to feature number 85, t1583
2023-03-15 14:35:03 INFO::Fitting model to feature number 86, t71999
2023-03-15 14:35:03 INFO::Counting total values for each feature
2023-03-15 14:35:03 INFO::Writing residuals to file maaslin_outputs/dose1_shedding_India_adjusted/residuals.rds
2023-03-15 14:35:03 INFO::Writing fitted values to file maaslin_outputs/dose1_shedding_India_adjusted/fitted.rds
2023-03-15 14:35:03 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_India_adjusted/all_results.tsv
2023-03-15 14:35:03 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_India_adjusted/significant_results.tsv
2023-03-15 14:35:03 INFO::Writing heatmap of significant results to file: maaslin_outputs/dose1_shedding_India_adjusted/heatmap.pdf

[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:35:10 INFO::Writing function arguments to log file
2023-03-15 14:35:10 INFO::Verifying options selected are valid
2023-03-15 14:35:10 INFO::Determining format of input files
2023-03-15 14:35:10 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:35:10 INFO::Formula for fixed effects: expr ~  dose1_shedding
2023-03-15 14:35:10 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:35:10 INFO::Total samples in data: 147
2023-03-15 14:35:10 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:35:10 INFO::Total filtered features: 0
2023-03-15 14:35:10 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:35:10 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:35:10 INFO::Filtered feature names from variance filtering:
2023-03-15 14:35:10 INFO::Running selected normalization method: NONE
2023-03-15 14:35:10 INFO::Bypass z-score application to metadata
2023-03-15 14:35:10 INFO::Running selected transform method: AST
2023-03-15 14:35:10 INFO::Running selected analysis method: LM
2023-03-15 14:35:10 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:35:10 INFO::Fitting model to feature number 2, t562
2023-03-15 14:35:10 INFO::Fitting model to feature number 3, t573
2023-03-15 14:35:10 INFO::Fitting model to feature number 4, t817
2023-03-15 14:35:10 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:35:10 INFO::Fitting model to feature number 6, t823
2023-03-15 14:35:10 INFO::Fitting model to feature number 7, t821
2023-03-15 14:35:10 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:35:10 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:35:10 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:35:10 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:35:10 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:35:10 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:35:10 INFO::Fitting model to feature number 14, t550
2023-03-15 14:35:10 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:35:10 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:35:10 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:35:10 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:35:10 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:35:10 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:35:10 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:35:10 INFO::Fitting model to feature number 22, t729
2023-03-15 14:35:10 INFO::Fitting model to feature number 23, t907
2023-03-15 14:35:10 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:35:10 INFO::Fitting model to feature number 25, t853
2023-03-15 14:35:10 INFO::Fitting model to feature number 26, t197
2023-03-15 14:35:10 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:35:10 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:35:10 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:35:10 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:35:10 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:35:10 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:35:10 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:35:10 INFO::Fitting model to feature number 34, t584
2023-03-15 14:35:10 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:35:10 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:35:10 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:35:10 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:35:10 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:35:10 INFO::Fitting model to feature number 40, t624
2023-03-15 14:35:10 INFO::Fitting model to feature number 41, t545
2023-03-15 14:35:10 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:35:10 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:35:10 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:35:10 INFO::Fitting model to feature number 45, t582
2023-03-15 14:35:10 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:35:10 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:35:10 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:35:10 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:35:10 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:35:10 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:35:10 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:35:10 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:35:10 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:35:10 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:35:10 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:35:10 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:35:10 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:35:10 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:35:10 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:35:10 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:35:10 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:35:10 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:35:10 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:35:10 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:35:10 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:35:10 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:35:10 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:35:10 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:35:10 INFO::Fitting model to feature number 70, t287
2023-03-15 14:35:10 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:35:10 INFO::Fitting model to feature number 72, t901
2023-03-15 14:35:10 INFO::Fitting model to feature number 73, t604330
2023-03-15 14:35:10 INFO::Fitting model to feature number 74, t143361
2023-03-15 14:35:10 INFO::Fitting model to feature number 75, t2823316
2023-03-15 14:35:10 INFO::Fitting model to feature number 76, t2093857
2023-03-15 14:35:10 INFO::Fitting model to feature number 77, t84030
2023-03-15 14:35:10 INFO::Fitting model to feature number 78, t1464
2023-03-15 14:35:10 INFO::Fitting model to feature number 79, t1297617
2023-03-15 14:35:10 INFO::Fitting model to feature number 80, t2714355
2023-03-15 14:35:10 INFO::Fitting model to feature number 81, t83655
2023-03-15 14:35:10 INFO::Fitting model to feature number 82, t2774055
2023-03-15 14:35:10 INFO::Fitting model to feature number 83, t1270
2023-03-15 14:35:10 INFO::Fitting model to feature number 84, t39485
2023-03-15 14:35:10 INFO::Fitting model to feature number 85, t1583
2023-03-15 14:35:11 INFO::Fitting model to feature number 86, t71999
2023-03-15 14:35:11 INFO::Counting total values for each feature
2023-03-15 14:35:11 INFO::Writing residuals to file maaslin_outputs/dose1_shedding_India (exposed)_unadjusted/residuals.rds
2023-03-15 14:35:11 INFO::Writing fitted values to file maaslin_outputs/dose1_shedding_India (exposed)_unadjusted/fitted.rds
2023-03-15 14:35:11 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_India (exposed)_unadjusted/all_results.tsv
2023-03-15 14:35:11 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_India (exposed)_unadjusted/significant_results.tsv
2023-03-15 14:35:11 INFO::Writing heatmap of significant results to file: maaslin_outputs/dose1_shedding_India (exposed)_unadjusted/heatmap.pdf
[1] "There are no associations to plot!"
[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:35:11 INFO::Writing function arguments to log file
2023-03-15 14:35:11 INFO::Verifying options selected are valid
2023-03-15 14:35:11 INFO::Determining format of input files
2023-03-15 14:35:11 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:35:11 INFO::Formula for fixed effects: expr ~  dose1_shedding + age_at_first_dose + antibiotic_exposure + birth_weight + breastfed_child + mode_delivery
2023-03-15 14:35:11 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:35:11 INFO::Total samples in data: 147
2023-03-15 14:35:11 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:35:11 INFO::Total filtered features: 0
2023-03-15 14:35:11 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:35:11 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:35:11 INFO::Filtered feature names from variance filtering:
2023-03-15 14:35:11 INFO::Running selected normalization method: NONE
2023-03-15 14:35:11 INFO::Bypass z-score application to metadata
2023-03-15 14:35:11 INFO::Running selected transform method: AST
2023-03-15 14:35:11 INFO::Running selected analysis method: LM
2023-03-15 14:35:11 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:35:11 INFO::Fitting model to feature number 2, t562
2023-03-15 14:35:11 INFO::Fitting model to feature number 3, t573
2023-03-15 14:35:11 INFO::Fitting model to feature number 4, t817
2023-03-15 14:35:11 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:35:11 INFO::Fitting model to feature number 6, t823
2023-03-15 14:35:11 INFO::Fitting model to feature number 7, t821
2023-03-15 14:35:11 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:35:11 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:35:11 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:35:11 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:35:11 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:35:11 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:35:11 INFO::Fitting model to feature number 14, t550
2023-03-15 14:35:11 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:35:11 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:35:11 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:35:11 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:35:11 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:35:11 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:35:11 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:35:11 INFO::Fitting model to feature number 22, t729
2023-03-15 14:35:11 INFO::Fitting model to feature number 23, t907
2023-03-15 14:35:11 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:35:11 INFO::Fitting model to feature number 25, t853
2023-03-15 14:35:11 INFO::Fitting model to feature number 26, t197
2023-03-15 14:35:11 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:35:11 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:35:11 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:35:11 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:35:11 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:35:11 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:35:11 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:35:11 INFO::Fitting model to feature number 34, t584
2023-03-15 14:35:11 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:35:11 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:35:11 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:35:11 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:35:11 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:35:11 INFO::Fitting model to feature number 40, t624
2023-03-15 14:35:11 INFO::Fitting model to feature number 41, t545
2023-03-15 14:35:11 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:35:11 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:35:11 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:35:11 INFO::Fitting model to feature number 45, t582
2023-03-15 14:35:11 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:35:11 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:35:11 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:35:11 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:35:11 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:35:11 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:35:11 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:35:11 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:35:11 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:35:11 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:35:11 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:35:11 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:35:11 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:35:11 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:35:11 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:35:11 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:35:11 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:35:11 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:35:11 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:35:11 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:35:11 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:35:11 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:35:11 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:35:11 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:35:11 INFO::Fitting model to feature number 70, t287
2023-03-15 14:35:11 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:35:11 INFO::Fitting model to feature number 72, t901
2023-03-15 14:35:11 INFO::Fitting model to feature number 73, t604330
2023-03-15 14:35:11 INFO::Fitting model to feature number 74, t143361
2023-03-15 14:35:11 INFO::Fitting model to feature number 75, t2823316
2023-03-15 14:35:11 INFO::Fitting model to feature number 76, t2093857
2023-03-15 14:35:11 INFO::Fitting model to feature number 77, t84030
2023-03-15 14:35:11 INFO::Fitting model to feature number 78, t1464
2023-03-15 14:35:11 INFO::Fitting model to feature number 79, t1297617
2023-03-15 14:35:11 INFO::Fitting model to feature number 80, t2714355
2023-03-15 14:35:11 INFO::Fitting model to feature number 81, t83655
2023-03-15 14:35:11 INFO::Fitting model to feature number 82, t2774055
2023-03-15 14:35:11 INFO::Fitting model to feature number 83, t1270
2023-03-15 14:35:11 INFO::Fitting model to feature number 84, t39485
2023-03-15 14:35:11 INFO::Fitting model to feature number 85, t1583
2023-03-15 14:35:11 INFO::Fitting model to feature number 86, t71999
2023-03-15 14:35:11 INFO::Counting total values for each feature
2023-03-15 14:35:11 INFO::Writing residuals to file maaslin_outputs/dose1_shedding_India (exposed)_adjusted/residuals.rds
2023-03-15 14:35:11 INFO::Writing fitted values to file maaslin_outputs/dose1_shedding_India (exposed)_adjusted/fitted.rds
2023-03-15 14:35:11 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_India (exposed)_adjusted/all_results.tsv
2023-03-15 14:35:11 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_India (exposed)_adjusted/significant_results.tsv
2023-03-15 14:35:11 INFO::Writing heatmap of significant results to file: maaslin_outputs/dose1_shedding_India (exposed)_adjusted/heatmap.pdf

[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:35:24 INFO::Writing function arguments to log file
2023-03-15 14:35:24 INFO::Verifying options selected are valid
2023-03-15 14:35:24 INFO::Determining format of input files
2023-03-15 14:35:24 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:35:24 INFO::Formula for fixed effects: expr ~  dose1_shedding
2023-03-15 14:35:24 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:35:24 INFO::Total samples in data: 132
2023-03-15 14:35:24 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:35:24 INFO::Total filtered features: 0
2023-03-15 14:35:24 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:35:24 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:35:24 INFO::Filtered feature names from variance filtering:
2023-03-15 14:35:24 INFO::Running selected normalization method: NONE
2023-03-15 14:35:24 INFO::Bypass z-score application to metadata
2023-03-15 14:35:24 INFO::Running selected transform method: AST
2023-03-15 14:35:24 INFO::Running selected analysis method: LM
2023-03-15 14:35:24 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:35:24 INFO::Fitting model to feature number 2, t562
2023-03-15 14:35:24 INFO::Fitting model to feature number 3, t573
2023-03-15 14:35:24 INFO::Fitting model to feature number 4, t817
2023-03-15 14:35:24 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:35:24 INFO::Fitting model to feature number 6, t823
2023-03-15 14:35:24 INFO::Fitting model to feature number 7, t821
2023-03-15 14:35:24 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:35:24 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:35:24 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:35:24 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:35:24 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:35:24 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:35:24 INFO::Fitting model to feature number 14, t550
2023-03-15 14:35:24 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:35:24 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:35:24 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:35:24 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:35:24 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:35:24 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:35:24 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:35:24 INFO::Fitting model to feature number 22, t729
2023-03-15 14:35:24 INFO::Fitting model to feature number 23, t907
2023-03-15 14:35:24 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:35:24 INFO::Fitting model to feature number 25, t853
2023-03-15 14:35:24 INFO::Fitting model to feature number 26, t197
2023-03-15 14:35:24 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:35:24 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:35:24 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:35:24 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:35:24 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:35:24 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:35:24 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:35:24 INFO::Fitting model to feature number 34, t584
2023-03-15 14:35:24 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:35:24 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:35:24 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:35:24 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:35:24 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:35:24 INFO::Fitting model to feature number 40, t624
2023-03-15 14:35:24 INFO::Fitting model to feature number 41, t545
2023-03-15 14:35:24 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:35:24 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:35:24 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:35:24 INFO::Fitting model to feature number 45, t582
2023-03-15 14:35:24 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:35:24 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:35:24 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:35:24 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:35:24 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:35:24 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:35:24 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:35:24 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:35:24 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:35:24 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:35:24 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:35:24 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:35:24 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:35:24 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:35:24 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:35:24 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:35:24 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:35:24 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:35:24 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:35:24 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:35:24 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:35:24 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:35:24 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:35:25 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:35:25 INFO::Fitting model to feature number 70, t287
2023-03-15 14:35:25 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:35:25 INFO::Fitting model to feature number 72, t604330
2023-03-15 14:35:25 INFO::Fitting model to feature number 73, t143361
2023-03-15 14:35:25 INFO::Fitting model to feature number 74, t2823316
2023-03-15 14:35:25 INFO::Fitting model to feature number 75, t2093857
2023-03-15 14:35:25 INFO::Fitting model to feature number 76, t84030
2023-03-15 14:35:25 INFO::Fitting model to feature number 77, t1464
2023-03-15 14:35:25 INFO::Fitting model to feature number 78, t1297617
2023-03-15 14:35:25 INFO::Fitting model to feature number 79, t2714355
2023-03-15 14:35:25 INFO::Fitting model to feature number 80, t83655
2023-03-15 14:35:25 INFO::Fitting model to feature number 81, t2774055
2023-03-15 14:35:25 INFO::Fitting model to feature number 82, t1270
2023-03-15 14:35:25 INFO::Fitting model to feature number 83, t39485
2023-03-15 14:35:25 INFO::Fitting model to feature number 84, t1583
2023-03-15 14:35:25 INFO::Fitting model to feature number 85, t71999
2023-03-15 14:35:25 INFO::Counting total values for each feature
2023-03-15 14:35:25 INFO::Writing residuals to file maaslin_outputs/dose1_shedding_India (unexposed)_unadjusted/residuals.rds
2023-03-15 14:35:25 INFO::Writing fitted values to file maaslin_outputs/dose1_shedding_India (unexposed)_unadjusted/fitted.rds
2023-03-15 14:35:25 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_India (unexposed)_unadjusted/all_results.tsv
2023-03-15 14:35:25 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_India (unexposed)_unadjusted/significant_results.tsv
2023-03-15 14:35:25 INFO::Writing heatmap of significant results to file: maaslin_outputs/dose1_shedding_India (unexposed)_unadjusted/heatmap.pdf
[1] "There are no associations to plot!"
[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:35:25 INFO::Writing function arguments to log file
2023-03-15 14:35:25 INFO::Verifying options selected are valid
2023-03-15 14:35:25 INFO::Determining format of input files
2023-03-15 14:35:25 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:35:25 INFO::Formula for fixed effects: expr ~  dose1_shedding + age_at_first_dose + antibiotic_exposure + birth_weight + breastfed_child + mode_delivery
2023-03-15 14:35:25 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:35:25 INFO::Total samples in data: 132
2023-03-15 14:35:25 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:35:25 INFO::Total filtered features: 0
2023-03-15 14:35:25 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:35:25 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:35:25 INFO::Filtered feature names from variance filtering:
2023-03-15 14:35:25 INFO::Running selected normalization method: NONE
2023-03-15 14:35:25 INFO::Bypass z-score application to metadata
2023-03-15 14:35:25 INFO::Running selected transform method: AST
2023-03-15 14:35:25 INFO::Running selected analysis method: LM
2023-03-15 14:35:25 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:35:25 INFO::Fitting model to feature number 2, t562
2023-03-15 14:35:25 INFO::Fitting model to feature number 3, t573
2023-03-15 14:35:25 INFO::Fitting model to feature number 4, t817
2023-03-15 14:35:25 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:35:25 INFO::Fitting model to feature number 6, t823
2023-03-15 14:35:25 INFO::Fitting model to feature number 7, t821
2023-03-15 14:35:25 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:35:25 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:35:25 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:35:25 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:35:25 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:35:25 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:35:25 INFO::Fitting model to feature number 14, t550
2023-03-15 14:35:25 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:35:25 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:35:25 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:35:25 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:35:25 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:35:25 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:35:25 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:35:25 INFO::Fitting model to feature number 22, t729
2023-03-15 14:35:25 INFO::Fitting model to feature number 23, t907
2023-03-15 14:35:25 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:35:25 INFO::Fitting model to feature number 25, t853
2023-03-15 14:35:25 INFO::Fitting model to feature number 26, t197
2023-03-15 14:35:25 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:35:25 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:35:25 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:35:25 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:35:25 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:35:25 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:35:25 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:35:25 INFO::Fitting model to feature number 34, t584
2023-03-15 14:35:25 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:35:25 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:35:25 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:35:25 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:35:25 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:35:25 INFO::Fitting model to feature number 40, t624
2023-03-15 14:35:25 INFO::Fitting model to feature number 41, t545
2023-03-15 14:35:25 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:35:25 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:35:25 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:35:25 INFO::Fitting model to feature number 45, t582
2023-03-15 14:35:25 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:35:25 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:35:25 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:35:25 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:35:25 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:35:25 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:35:25 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:35:25 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:35:25 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:35:25 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:35:25 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:35:25 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:35:25 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:35:25 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:35:25 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:35:25 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:35:25 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:35:25 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:35:25 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:35:25 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:35:25 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:35:25 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:35:25 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:35:25 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:35:25 INFO::Fitting model to feature number 70, t287
2023-03-15 14:35:25 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:35:25 INFO::Fitting model to feature number 72, t604330
2023-03-15 14:35:25 INFO::Fitting model to feature number 73, t143361
2023-03-15 14:35:25 INFO::Fitting model to feature number 74, t2823316
2023-03-15 14:35:25 INFO::Fitting model to feature number 75, t2093857
2023-03-15 14:35:25 INFO::Fitting model to feature number 76, t84030
2023-03-15 14:35:25 INFO::Fitting model to feature number 77, t1464
2023-03-15 14:35:25 INFO::Fitting model to feature number 78, t1297617
2023-03-15 14:35:25 INFO::Fitting model to feature number 79, t2714355
2023-03-15 14:35:25 INFO::Fitting model to feature number 80, t83655
2023-03-15 14:35:25 INFO::Fitting model to feature number 81, t2774055
2023-03-15 14:35:25 INFO::Fitting model to feature number 82, t1270
2023-03-15 14:35:25 INFO::Fitting model to feature number 83, t39485
2023-03-15 14:35:25 INFO::Fitting model to feature number 84, t1583
2023-03-15 14:35:25 INFO::Fitting model to feature number 85, t71999
2023-03-15 14:35:25 INFO::Counting total values for each feature
2023-03-15 14:35:25 INFO::Writing residuals to file maaslin_outputs/dose1_shedding_India (unexposed)_adjusted/residuals.rds
2023-03-15 14:35:25 INFO::Writing fitted values to file maaslin_outputs/dose1_shedding_India (unexposed)_adjusted/fitted.rds
2023-03-15 14:35:26 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_India (unexposed)_adjusted/all_results.tsv
2023-03-15 14:35:26 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_India (unexposed)_adjusted/significant_results.tsv
2023-03-15 14:35:26 INFO::Writing heatmap of significant results to file: maaslin_outputs/dose1_shedding_India (unexposed)_adjusted/heatmap.pdf

[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:35:33 INFO::Writing function arguments to log file
2023-03-15 14:35:33 INFO::Verifying options selected are valid
2023-03-15 14:35:33 INFO::Determining format of input files
2023-03-15 14:35:33 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:35:33 INFO::Formula for fixed effects: expr ~  dose1_shedding
2023-03-15 14:35:33 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:35:33 INFO::Total samples in data: 47
2023-03-15 14:35:33 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:35:33 INFO::Total filtered features: 0
2023-03-15 14:35:33 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:35:33 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:35:33 INFO::Filtered feature names from variance filtering:
2023-03-15 14:35:33 INFO::Running selected normalization method: NONE
2023-03-15 14:35:33 INFO::Bypass z-score application to metadata
2023-03-15 14:35:33 INFO::Running selected transform method: AST
2023-03-15 14:35:33 INFO::Running selected analysis method: LM
2023-03-15 14:35:33 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:35:33 INFO::Fitting model to feature number 2, t562
2023-03-15 14:35:33 INFO::Fitting model to feature number 3, t573
2023-03-15 14:35:33 INFO::Fitting model to feature number 4, t817
2023-03-15 14:35:33 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:35:33 INFO::Fitting model to feature number 6, t823
2023-03-15 14:35:33 INFO::Fitting model to feature number 7, t821
2023-03-15 14:35:33 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:35:33 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:35:34 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:35:34 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:35:34 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:35:34 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:35:34 INFO::Fitting model to feature number 14, t550
2023-03-15 14:35:34 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:35:34 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:35:34 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:35:34 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:35:34 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:35:34 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:35:34 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:35:34 INFO::Fitting model to feature number 22, t729
2023-03-15 14:35:34 INFO::Fitting model to feature number 23, t907
2023-03-15 14:35:34 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:35:34 INFO::Fitting model to feature number 25, t853
2023-03-15 14:35:34 INFO::Fitting model to feature number 26, t197
2023-03-15 14:35:34 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:35:34 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:35:34 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:35:34 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:35:34 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:35:34 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:35:34 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:35:34 INFO::Fitting model to feature number 34, t584
2023-03-15 14:35:34 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:35:34 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:35:34 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:35:34 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:35:34 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:35:34 INFO::Fitting model to feature number 40, t624
2023-03-15 14:35:34 INFO::Fitting model to feature number 41, t545
2023-03-15 14:35:34 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:35:34 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:35:34 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:35:34 INFO::Fitting model to feature number 45, t582
2023-03-15 14:35:34 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:35:34 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:35:34 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:35:34 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:35:34 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:35:34 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:35:34 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:35:34 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:35:34 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:35:34 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:35:34 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:35:34 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:35:34 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:35:34 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:35:34 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:35:34 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:35:34 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:35:34 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:35:34 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:35:34 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:35:34 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:35:34 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:35:34 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:35:34 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:35:34 INFO::Fitting model to feature number 70, t287
2023-03-15 14:35:34 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:35:34 INFO::Fitting model to feature number 72, t901
2023-03-15 14:35:34 INFO::Fitting model to feature number 73, t604330
2023-03-15 14:35:34 INFO::Fitting model to feature number 74, t143361
2023-03-15 14:35:34 INFO::Fitting model to feature number 75, t2823316
2023-03-15 14:35:34 INFO::Fitting model to feature number 76, t2093857
2023-03-15 14:35:34 INFO::Fitting model to feature number 77, t84030
2023-03-15 14:35:34 INFO::Fitting model to feature number 78, t1464
2023-03-15 14:35:34 INFO::Fitting model to feature number 79, t1297617
2023-03-15 14:35:34 INFO::Fitting model to feature number 80, t2714355
2023-03-15 14:35:34 INFO::Fitting model to feature number 81, t83655
2023-03-15 14:35:34 INFO::Fitting model to feature number 82, t2774055
2023-03-15 14:35:34 INFO::Fitting model to feature number 83, t1270
2023-03-15 14:35:34 INFO::Fitting model to feature number 84, t39485
2023-03-15 14:35:34 INFO::Fitting model to feature number 85, t1583
2023-03-15 14:35:34 INFO::Fitting model to feature number 86, t71999
2023-03-15 14:35:34 INFO::Counting total values for each feature
2023-03-15 14:35:34 INFO::Writing residuals to file maaslin_outputs/dose1_shedding_Malawi_unadjusted/residuals.rds
2023-03-15 14:35:34 INFO::Writing fitted values to file maaslin_outputs/dose1_shedding_Malawi_unadjusted/fitted.rds
2023-03-15 14:35:34 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_Malawi_unadjusted/all_results.tsv
2023-03-15 14:35:34 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_Malawi_unadjusted/significant_results.tsv
2023-03-15 14:35:34 INFO::Writing heatmap of significant results to file: maaslin_outputs/dose1_shedding_Malawi_unadjusted/heatmap.pdf
[1] "There are no associations to plot!"
[1] "Creating output folder"
[1] "Creating output figures folder"
2023-03-15 14:35:34 INFO::Writing function arguments to log file
2023-03-15 14:35:34 INFO::Verifying options selected are valid
2023-03-15 14:35:34 INFO::Determining format of input files
2023-03-15 14:35:34 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 14:35:34 INFO::Formula for fixed effects: expr ~  dose1_shedding + age_at_first_dose + antibiotic_exposure + birth_weight + breastfed_child
2023-03-15 14:35:34 INFO::Filter data based on min abundance and min prevalence
2023-03-15 14:35:34 INFO::Total samples in data: 47
2023-03-15 14:35:34 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-03-15 14:35:34 INFO::Total filtered features: 0
2023-03-15 14:35:34 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 14:35:34 INFO::Total filtered features with variance filtering: 0
2023-03-15 14:35:34 INFO::Filtered feature names from variance filtering:
2023-03-15 14:35:34 INFO::Running selected normalization method: NONE
2023-03-15 14:35:34 INFO::Bypass z-score application to metadata
2023-03-15 14:35:34 INFO::Running selected transform method: AST
2023-03-15 14:35:34 INFO::Running selected analysis method: LM
2023-03-15 14:35:34 INFO::Fitting model to feature number 1, t216816
2023-03-15 14:35:34 INFO::Fitting model to feature number 2, t562
2023-03-15 14:35:34 INFO::Fitting model to feature number 3, t573
2023-03-15 14:35:34 INFO::Fitting model to feature number 4, t817
2023-03-15 14:35:34 INFO::Fitting model to feature number 5, t1316412
2023-03-15 14:35:34 INFO::Fitting model to feature number 6, t823
2023-03-15 14:35:34 INFO::Fitting model to feature number 7, t821
2023-03-15 14:35:34 INFO::Fitting model to feature number 8, t29466
2023-03-15 14:35:34 INFO::Fitting model to feature number 9, t33038
2023-03-15 14:35:34 INFO::Fitting model to feature number 10, t1351
2023-03-15 14:35:34 INFO::Fitting model to feature number 11, t1596
2023-03-15 14:35:34 INFO::Fitting model to feature number 12, t239935
2023-03-15 14:35:34 INFO::Fitting model to feature number 13, t74426
2023-03-15 14:35:34 INFO::Fitting model to feature number 14, t550
2023-03-15 14:35:34 INFO::Fitting model to feature number 15, t165179
2023-03-15 14:35:34 INFO::Fitting model to feature number 16, t1492
2023-03-15 14:35:34 INFO::Fitting model to feature number 17, t1613
2023-03-15 14:35:34 INFO::Fitting model to feature number 18, t1624
2023-03-15 14:35:34 INFO::Fitting model to feature number 19, t1290
2023-03-15 14:35:34 INFO::Fitting model to feature number 20, t43675
2023-03-15 14:35:34 INFO::Fitting model to feature number 21, t437897
2023-03-15 14:35:34 INFO::Fitting model to feature number 22, t729
2023-03-15 14:35:34 INFO::Fitting model to feature number 23, t907
2023-03-15 14:35:35 INFO::Fitting model to feature number 24, t292800
2023-03-15 14:35:35 INFO::Fitting model to feature number 25, t853
2023-03-15 14:35:35 INFO::Fitting model to feature number 26, t197
2023-03-15 14:35:35 INFO::Fitting model to feature number 27, t40545
2023-03-15 14:35:35 INFO::Fitting model to feature number 28, t187327
2023-03-15 14:35:35 INFO::Fitting model to feature number 29, t208479
2023-03-15 14:35:35 INFO::Fitting model to feature number 30, t1547
2023-03-15 14:35:35 INFO::Fitting model to feature number 31, t1550024
2023-03-15 14:35:35 INFO::Fitting model to feature number 32, t33010
2023-03-15 14:35:35 INFO::Fitting model to feature number 33, t47715
2023-03-15 14:35:35 INFO::Fitting model to feature number 34, t584
2023-03-15 14:35:35 INFO::Fitting model to feature number 35, t1358
2023-03-15 14:35:35 INFO::Fitting model to feature number 36, t28901
2023-03-15 14:35:35 INFO::Fitting model to feature number 37, t202956
2023-03-15 14:35:35 INFO::Fitting model to feature number 38, t84112
2023-03-15 14:35:35 INFO::Fitting model to feature number 39, t1496
2023-03-15 14:35:35 INFO::Fitting model to feature number 40, t624
2023-03-15 14:35:35 INFO::Fitting model to feature number 41, t545
2023-03-15 14:35:35 INFO::Fitting model to feature number 42, t2003188
2023-03-15 14:35:35 INFO::Fitting model to feature number 43, t1590
2023-03-15 14:35:35 INFO::Fitting model to feature number 44, t1834196
2023-03-15 14:35:35 INFO::Fitting model to feature number 45, t582
2023-03-15 14:35:35 INFO::Fitting model to feature number 46, t2109685
2023-03-15 14:35:35 INFO::Fitting model to feature number 47, t328813
2023-03-15 14:35:35 INFO::Fitting model to feature number 48, t649756
2023-03-15 14:35:35 INFO::Fitting model to feature number 49, t111015
2023-03-15 14:35:35 INFO::Fitting model to feature number 50, t1736
2023-03-15 14:35:35 INFO::Fitting model to feature number 51, t28118
2023-03-15 14:35:35 INFO::Fitting model to feature number 52, t1660
2023-03-15 14:35:35 INFO::Fitting model to feature number 53, t2479767
2023-03-15 14:35:35 INFO::Fitting model to feature number 54, t28141
2023-03-15 14:35:35 INFO::Fitting model to feature number 55, t2582419
2023-03-15 14:35:35 INFO::Fitting model to feature number 56, t2823317
2023-03-15 14:35:35 INFO::Fitting model to feature number 57, t1379
2023-03-15 14:35:35 INFO::Fitting model to feature number 58, t166486
2023-03-15 14:35:35 INFO::Fitting model to feature number 59, t1382
2023-03-15 14:35:35 INFO::Fitting model to feature number 60, t410072
2023-03-15 14:35:35 INFO::Fitting model to feature number 61, t2093856
2023-03-15 14:35:35 INFO::Fitting model to feature number 62, t1260
2023-03-15 14:35:35 INFO::Fitting model to feature number 63, t1335613
2023-03-15 14:35:35 INFO::Fitting model to feature number 64, t161879
2023-03-15 14:35:35 INFO::Fitting model to feature number 65, t69966
2023-03-15 14:35:35 INFO::Fitting model to feature number 66, t39488
2023-03-15 14:35:35 INFO::Fitting model to feature number 67, t40324
2023-03-15 14:35:35 INFO::Fitting model to feature number 68, t1667168
2023-03-15 14:35:35 INFO::Fitting model to feature number 69, t34062
2023-03-15 14:35:35 INFO::Fitting model to feature number 70, t287
2023-03-15 14:35:35 INFO::Fitting model to feature number 71, t54005
2023-03-15 14:35:35 INFO::Fitting model to feature number 72, t901
2023-03-15 14:35:35 INFO::Fitting model to feature number 73, t604330
2023-03-15 14:35:35 INFO::Fitting model to feature number 74, t143361
2023-03-15 14:35:35 INFO::Fitting model to feature number 75, t2823316
2023-03-15 14:35:35 INFO::Fitting model to feature number 76, t2093857
2023-03-15 14:35:35 INFO::Fitting model to feature number 77, t84030
2023-03-15 14:35:35 INFO::Fitting model to feature number 78, t1464
2023-03-15 14:35:35 INFO::Fitting model to feature number 79, t1297617
2023-03-15 14:35:35 INFO::Fitting model to feature number 80, t2714355
2023-03-15 14:35:35 INFO::Fitting model to feature number 81, t83655
2023-03-15 14:35:35 INFO::Fitting model to feature number 82, t2774055
2023-03-15 14:35:35 INFO::Fitting model to feature number 83, t1270
2023-03-15 14:35:35 INFO::Fitting model to feature number 84, t39485
2023-03-15 14:35:35 INFO::Fitting model to feature number 85, t1583
2023-03-15 14:35:35 INFO::Fitting model to feature number 86, t71999
2023-03-15 14:35:35 INFO::Counting total values for each feature
2023-03-15 14:35:35 INFO::Writing residuals to file maaslin_outputs/dose1_shedding_Malawi_adjusted/residuals.rds
2023-03-15 14:35:35 INFO::Writing fitted values to file maaslin_outputs/dose1_shedding_Malawi_adjusted/fitted.rds
2023-03-15 14:35:35 INFO::Writing all results to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_Malawi_adjusted/all_results.tsv
2023-03-15 14:35:35 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.200000 ) to file (ordered by increasing q-values): maaslin_outputs/dose1_shedding_Malawi_adjusted/significant_results.tsv
2023-03-15 14:35:35 INFO::Writing heatmap of significant results to file: maaslin_outputs/dose1_shedding_Malawi_adjusted/heatmap.pdf

     country n_tested_fisher n_signif_fisher n_tested_lr n_signif_lr
1        MLW              78               0          78           0
2 IND (neo-)              80               0          80           0
3 IND (neo+)              80               0          80           0
4        IND              81               0          81           0
  n_tested_maaslin n_signif_maaslin
1               86                0
2               85                0
3               86                0
4               86                0

     country n_neg n_equal n_pos total proportion_neg
1        IND    62       0    19    81          76.5%
2 IND (neo+)    53       1    26    80          66.2%
3 IND (neo-)    61       0    19    80          76.2%
4        MLW    53       0    25    78          67.9%

                       [,1]
IND            3.673533e-07
MLW            1.909140e-04
IND_exposed    1.775874e-03
IND_nonexposed 1.139271e-06

                      [,1]
IND            0.626557662
MLW            0.740220195
IND_exposed    0.001082141
IND_nonexposed 0.267608811

     country n_neg n_equal n_pos total proportion_neg
1        IND    43       0    43    86            50%
2 IND (neo+)    62       0    24    86          72.1%
3 IND (neo-)    35       0    50    85          41.2%
4        MLW    39       0    47    86          45.3%

      subset     N_features FDR p<0.2 unadjusted FDR p<0.2 adjusted
1        IND 86 (43 +/43 -)          0 (0 +/0 -)        0 (0 +/0 -)
2 IND (neo+) 86 (24 +/62 -)          0 (0 +/0 -)        0 (0 +/0 -)
3 IND (neo-) 85 (50 +/35 -)          0 (0 +/0 -)        0 (0 +/0 -)
4        MLW 86 (47 +/39 -)          0 (0 +/0 -)        0 (0 +/0 -)

                                  Fisher p         LR p  LR (adj) p    Wilcox p
Fisher p                       1.000000000  0.992090623  0.93050869  0.66336738
LR p                           0.992090623  1.000000000  0.94234417  0.66551491
LR (adj) p                     0.930508688  0.942344173  1.00000000  0.63188799
Wilcox p                       0.663367384  0.665514905  0.63188799  1.00000000
Maaslin p                     -0.177649758 -0.172177055 -0.18678862  0.06210479
Maaslin (adj) p               -0.159887042 -0.152213189 -0.17511292  0.06309846
RF rank                        0.249355990  0.254200542  0.26262421  0.26054652
Inv. abs. Maaslin coef. (adj) -0.029536730 -0.025022584  0.01036585  0.04462511
Inv. abs. prev. diff.          0.961892407  0.965272300  0.93025095  0.61676418
Inv. abs. mean abund. diff.   -0.000723164 -0.002484192  0.04126016 -0.03787263
                                Maaslin p Maaslin (adj) p   RF rank
Fisher p                      -0.17764976     -0.15988704 0.2493560
LR p                          -0.17217706     -0.15221319 0.2542005
LR (adj) p                    -0.18678862     -0.17511292 0.2626242
Wilcox p                       0.06210479      0.06309846 0.2605465
Maaslin p                      1.00000000      0.96106594 0.1732385
Maaslin (adj) p                0.96106594      1.00000000 0.1904246
RF rank                        0.17323848      0.19042457 1.0000000
Inv. abs. Maaslin coef. (adj)  0.48073622      0.54661247 0.4971771
Inv. abs. prev. diff.         -0.20311477     -0.18838796 0.2319924
Inv. abs. mean abund. diff.    0.26689250      0.30733966 0.3796296
                              Inv. abs. Maaslin coef. (adj)
Fisher p                                        -0.02953673
LR p                                            -0.02502258
LR (adj) p                                       0.01036585
Wilcox p                                         0.04462511
Maaslin p                                        0.48073622
Maaslin (adj) p                                  0.54661247
RF rank                                          0.49717706
Inv. abs. Maaslin coef. (adj)                    1.00000000
Inv. abs. prev. diff.                           -0.05948321
Inv. abs. mean abund. diff.                      0.86851852
                              Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p                                 0.96189241                -0.000723164
LR p                                     0.96527230                -0.002484192
LR (adj) p                               0.93025095                 0.041260163
Wilcox p                                 0.61676418                -0.037872629
Maaslin p                               -0.20311477                 0.266892502
Maaslin (adj) p                         -0.18838796                 0.307339657
RF rank                                  0.23199241                 0.379629630
Inv. abs. Maaslin coef. (adj)           -0.05948321                 0.868518519
Inv. abs. prev. diff.                    1.00000000                -0.024823256
Inv. abs. mean abund. diff.             -0.02482326                 1.000000000

                               Fisher p      LR p LR (adj) p  Wilcox p
Fisher p                      1.0000000 0.9166754 0.79970312 0.7066152
LR p                          0.9166754 1.0000000 0.86467417 0.6647914
LR (adj) p                    0.7997031 0.8646742 1.00000000 0.5046648
Wilcox p                      0.7066152 0.6647914 0.50466479 1.0000000
Maaslin p                     0.2277497 0.1928739 0.08691983 0.4854665
Maaslin (adj) p               0.1879541 0.1382325 0.07538678 0.3638303
RF rank                       0.3351470 0.3330989 0.25686826 0.3398734
Inv. abs. Maaslin coef. (adj) 0.1900387 0.1683310 0.10131271 0.2022738
Inv. abs. prev. diff.         0.9467901 0.9284563 0.80371345 0.6934352
Inv. abs. mean abund. diff.   0.1582518 0.1481716 0.06223629 0.1531646
                               Maaslin p Maaslin (adj) p   RF rank
Fisher p                      0.22774968      0.18795414 0.3351470
LR p                          0.19287389      0.13823254 0.3330989
LR (adj) p                    0.08691983      0.07538678 0.2568683
Wilcox p                      0.48546648      0.36383029 0.3398734
Maaslin p                     1.00000000      0.80888420 0.2679794
Maaslin (adj) p               0.80888420      1.00000000 0.2543366
RF rank                       0.26797937      0.25433662 1.0000000
Inv. abs. Maaslin coef. (adj) 0.48926395      0.57653540 0.4527661
Inv. abs. prev. diff.         0.20235256      0.14240753 0.3156315
Inv. abs. mean abund. diff.   0.29889827      0.21851852 0.3879278
                              Inv. abs. Maaslin coef. (adj)
Fisher p                                          0.1900387
LR p                                              0.1683310
LR (adj) p                                        0.1013127
Wilcox p                                          0.2022738
Maaslin p                                         0.4892639
Maaslin (adj) p                                   0.5765354
RF rank                                           0.4527661
Inv. abs. Maaslin coef. (adj)                     1.0000000
Inv. abs. prev. diff.                             0.1795303
Inv. abs. mean abund. diff.                       0.8518987
                              Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p                                  0.9467901                  0.15825176
LR p                                      0.9284563                  0.14817159
LR (adj) p                                0.8037135                  0.06223629
Wilcox p                                  0.6934352                  0.15316456
Maaslin p                                 0.2023526                  0.29889827
Maaslin (adj) p                           0.1424075                  0.21851852
RF rank                                   0.3156315                  0.38792780
Inv. abs. Maaslin coef. (adj)             0.1795303                  0.85189873
Inv. abs. prev. diff.                     1.0000000                  0.16794922
Inv. abs. mean abund. diff.               0.1679492                  1.00000000

                                 Fisher p        LR p   LR (adj) p    Wilcox p
Fisher p                       1.00000000  0.99074288  0.938698789 0.722413186
LR p                           0.99074288  1.00000000  0.943266194 0.736560810
LR (adj) p                     0.93869879  0.94326619  1.000000000 0.677590248
Wilcox p                       0.72241319  0.73656081  0.677590248 1.000000000
Maaslin p                     -0.07855102 -0.07603186 -0.072737928 0.076324426
Maaslin (adj) p               -0.05322525 -0.04709357 -0.031692452 0.122386310
RF rank                        0.33149141  0.32375952  0.275246132 0.391209564
Inv. abs. Maaslin coef. (adj)  0.01880336  0.02611361  0.014838256 0.144233474
Inv. abs. prev. diff.          0.97001583  0.97378492  0.911397897 0.692254497
Inv. abs. mean abund. diff.    0.01615913  0.01993683  0.009634318 0.006962025
                                Maaslin p Maaslin (adj) p   RF rank
Fisher p                      -0.07855102     -0.05322525 0.3314914
LR p                          -0.07603186     -0.04709357 0.3237595
LR (adj) p                    -0.07273793     -0.03169245 0.2752461
Wilcox p                       0.07632443      0.12238631 0.3912096
Maaslin p                      1.00000000      0.91387717 0.1368026
Maaslin (adj) p                0.91387717      1.00000000 0.1156821
RF rank                        0.13680263      0.11568214 1.0000000
Inv. abs. Maaslin coef. (adj)  0.55527426      0.59864041 0.3707689
Inv. abs. prev. diff.         -0.12650913     -0.07256722 0.2655133
Inv. abs. mean abund. diff.    0.26052508      0.21228317 0.3313174
                              Inv. abs. Maaslin coef. (adj)
Fisher p                                         0.01880336
LR p                                             0.02611361
LR (adj) p                                       0.01483826
Wilcox p                                         0.14423347
Maaslin p                                        0.55527426
Maaslin (adj) p                                  0.59864041
RF rank                                          0.37076887
Inv. abs. Maaslin coef. (adj)                    1.00000000
Inv. abs. prev. diff.                           -0.02931524
Inv. abs. mean abund. diff.                      0.81394749
                              Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p                                 0.97001583                 0.016159134
LR p                                     0.97378492                 0.019936826
LR (adj) p                               0.91139790                 0.009634318
Wilcox p                                 0.69225450                 0.006962025
Maaslin p                               -0.12650913                 0.260525082
Maaslin (adj) p                         -0.07256722                 0.212283169
RF rank                                  0.26551328                 0.331317393
Inv. abs. Maaslin coef. (adj)           -0.02931524                 0.813947492
Inv. abs. prev. diff.                    1.00000000                -0.019750569
Inv. abs. mean abund. diff.             -0.01975057                 1.000000000

                                  Fisher p        LR p  LR (adj) p  Wilcox p
Fisher p                       1.000000000  0.57994302  0.41955041 0.4248948
LR p                           0.579943020  1.00000000  0.83640641 0.3448036
LR (adj) p                     0.419550414  0.83640641  1.00000000 0.3374474
Wilcox p                       0.424894762  0.34480360  0.33744736 1.0000000
Maaslin p                      0.041543055  0.02553305 -0.03564790 0.4279644
Maaslin (adj) p               -0.003749972  0.06034853 -0.04156603 0.2441230
RF rank                        0.282893279 -0.03817943 -0.09500626 0.2345882
Inv. abs. Maaslin coef. (adj)  0.081517244 -0.06242254 -0.05560263 0.1882295
Inv. abs. prev. diff.          0.928039983  0.75305465  0.60499590 0.4678556
Inv. abs. mean abund. diff.    0.183531782 -0.12862635 -0.08726716 0.1478901
                                Maaslin p Maaslin (adj) p     RF rank
Fisher p                       0.04154305    -0.003749972  0.28289328
LR p                           0.02553305     0.060348534 -0.03817943
LR (adj) p                    -0.03564790    -0.041566029 -0.09500626
Wilcox p                       0.42796444     0.244122966  0.23458820
Maaslin p                      1.00000000     0.832041376 -0.02975506
Maaslin (adj) p                0.83204138     1.000000000 -0.10269477
RF rank                       -0.02975506    -0.102694774  1.00000000
Inv. abs. Maaslin coef. (adj)  0.29321312     0.451434641  0.36926365
Inv. abs. prev. diff.          0.02482767    -0.018326694  0.11553785
Inv. abs. mean abund. diff.    0.12699958     0.135598579  0.42862201
                              Inv. abs. Maaslin coef. (adj)
Fisher p                                         0.08151724
LR p                                            -0.06242254
LR (adj) p                                      -0.05560263
Wilcox p                                         0.18822949
Maaslin p                                        0.29321312
Maaslin (adj) p                                  0.45143464
RF rank                                          0.36926365
Inv. abs. Maaslin coef. (adj)                    1.00000000
Inv. abs. prev. diff.                           -0.02547271
Inv. abs. mean abund. diff.                      0.83904703
                              Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p                                 0.92803998                  0.18353178
LR p                                     0.75305465                 -0.12862635
LR (adj) p                               0.60499590                 -0.08726716
Wilcox p                                 0.46785557                  0.14789008
Maaslin p                                0.02482767                  0.12699958
Maaslin (adj) p                         -0.01832669                  0.13559858
RF rank                                  0.11553785                  0.42862201
Inv. abs. Maaslin coef. (adj)           -0.02547271                  0.83904703
Inv. abs. prev. diff.                    1.00000000                  0.03170809
Inv. abs. mean abund. diff.              0.03170809                  1.00000000